3zso - Revision history

OCA at 11:11, 20 December 2023

OCA — Wed, 20 Dec 2023 11:11:45 GMT

←Older revision		Revision as of 11:11, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='3zso' size='340' side='right'caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3zso' size='340' side='right'caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aids_virus Aids~~ virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.75Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [https://pdbe.org/3zso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [https://www.ebi.ac.uk/pdbsum/3zso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [https://pdbe.org/3zso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [https://www.ebi.ac.uk/pdbsum/3zso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/POL_HV1N5 POL_HV1N5] Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation (By similarity). Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to play a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu (By similarity). Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity (By similarity). The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aids~~ virus]]	+	[[Category: Human immunodeficiency virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Coates~~, J A.V~~]]	+	[[Category: Coates JAV]]
-	[[Category: Deadman~~, J J~~]]	+	[[Category: Deadman JJ]]
-	[[Category: Dolezal, O]]	+	[[Category: Dolezal O]]
-	[[Category: Francis~~, C L~~]]	+	[[Category: Francis CL]]
-	[[Category: Jones~~, E D~~]]	+	[[Category: Jones ED]]
-	[[Category: Le, G]]	+	[[Category: Le G]]
-	[[Category: Newman, J]]	+	[[Category: Newman J]]
-	[[Category: Peat~~, T S~~]]	+	[[Category: Peat TS]]
-	[[Category: Rhodes~~, D I~~]]	+	[[Category: Rhodes DI]]
-	[[Category: Ryan~~, J H~~]]	+	[[Category: Ryan JH]]
-	[[Category: Savage~~, G P~~]]	+	[[Category: Savage GP]]
-	[[Category: Smith~~, J A~~]]	+	[[Category: Smith JA]]
-	[[Category: Thienthong, N]]	+	[[Category: Thienthong N]]
-	[[Category: Vandergraaff, N]]	+	[[Category: Vandergraaff N]]
-	~~[[Category: Aid]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:14, 18 August 2022

OCA — Thu, 18 Aug 2022 07:14:46 GMT

←Older revision		Revision as of 07:14, 18 August 2022
Line 3:		Line 3:
	<StructureSection load='3zso' size='340' side='right'caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3zso' size='340' side='right'caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aids_virus Aids virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aids_virus Aids virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [~~http~~://pdbe.org/3zso PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3zso PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [https://pdbe.org/3zso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [https://www.ebi.ac.uk/pdbsum/3zso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:11, 4 November 2020

OCA — Wed, 04 Nov 2020 08:11:52 GMT

←Older revision		Revision as of 08:11, 4 November 2020
Line 1:		Line 1:

	==Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design==		==Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design==
-	<StructureSection load='3zso' size='340' side='right' caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='3zso' size='340' side='right'caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aids_virus Aids virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aids_virus Aids virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [http://pdbe.org/3zso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [http://www.ebi.ac.uk/pdbsum/3zso PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [http://pdbe.org/3zso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [http://www.ebi.ac.uk/pdbsum/3zso PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Aids virus]]		[[Category: Aids virus]]
		+	[[Category: Large Structures]]
	[[Category: Coates, J A.V]]		[[Category: Coates, J A.V]]
	[[Category: Deadman, J J]]		[[Category: Deadman, J J]]

OCA at 11:08, 11 August 2016

OCA — Thu, 11 Aug 2016 11:08:33 GMT

←Older revision		Revision as of 11:08, 11 August 2016
Line 1:		Line 1:
		+
	==Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design==		==Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design==
	<StructureSection load='3zso' size='340' side='right' caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='3zso' size='340' side='right' caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus Human immunodeficiency~~ virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aids_virus Aids virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [http://www.ebi.ac.uk/pdbsum/3zso PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [http://pdbe.org/3zso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [http://www.ebi.ac.uk/pdbsum/3zso PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3zso ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3zso" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human immunodeficiency~~ virus]]	+	[[Category: Aids virus]]
	[[Category: Coates, J A.V]]		[[Category: Coates, J A.V]]
	[[Category: Deadman, J J]]		[[Category: Deadman, J J]]

OCA at 09:44, 4 January 2015

OCA — Sun, 04 Jan 2015 09:44:36 GMT

←Older revision		Revision as of 09:44, 4 January 2015
Line 1:		Line 1:
-	[[~~Image:~~3zso.~~png~~\|~~left~~\|~~200px~~]]	+	==Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design==
		+	<StructureSection load='3zso' size='340' side='right' caption='[[3zso]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ZSO FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=O2N:5-{[(2-{[BIS(4-METHOXYPHENYL)METHYL]CARBAMOYL}BENZYL)(PROP-2-EN-1-YL)AMINO]METHYL}-1,3-BENZODIOXOLE-4-CARBOXYLIC+ACID'>O2N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3zsq\|3zsq]], [[3zt2\|3zt2]], [[3zt3\|3zt3]], [[3zt4\|3zt4]], [[3zsw\|3zsw]], [[1hyz\|1hyz]], [[1hyv\|1hyv]], [[3zt1\|3zt1]], [[3zsx\|3zsx]], [[3zsz\|3zsz]], [[3zt0\|3zt0]], [[3zsy\|3zsy]], [[3zsv\|3zsv]], [[3zsr\|3zsr]]</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3zso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3zso OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3zso RCSB], [http://www.ebi.ac.uk/pdbsum/3zso PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A fragment-based screen against human immunodeficiency virus type 1 (HIV) integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF) binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.

-	~~{{STRUCTURE_3zso\| PDB=3zso \| SCENE= }}~~	+	Small Molecule Inhibitors of the LEDGF Site of Human Immunodeficiency Virus Integrase Identified by Fragment Screening and Structure Based Design.,Peat TS, Rhodes DI, Vandegraaff N, Le G, Smith JA, Clark LJ, Jones ED, Coates JA, Thienthong N, Newman J, Dolezal O, Mulder R, Ryan JH, Savage GP, Francis CL, Deadman JJ PLoS One. 2012;7(7):e40147. Epub 2012 Jul 10. PMID:22808106<ref>PMID:22808106</ref>

-	~~===Small molecule inhibitors~~ of the ~~LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_22808106}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3zso]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022808106<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Human immunodeficiency virus]]		[[Category: Human immunodeficiency virus]]
-	[[Category: Coates, J A.V.]]	+	[[Category: Coates, J A.V]]
-	[[Category: Deadman, J J.]]	+	[[Category: Deadman, J J]]
-	[[Category: Dolezal, O.]]	+	[[Category: Dolezal, O]]
-	[[Category: Francis, C L.]]	+	[[Category: Francis, C L]]
-	[[Category: Jones, E D.]]	+	[[Category: Jones, E D]]
-	[[Category: Le, G.]]	+	[[Category: Le, G]]
-	[[Category: Newman, J.]]	+	[[Category: Newman, J]]
-	[[Category: Peat, T S.]]	+	[[Category: Peat, T S]]
-	[[Category: Rhodes, D I.]]	+	[[Category: Rhodes, D I]]
-	[[Category: Ryan, J H.]]	+	[[Category: Ryan, J H]]
-	[[Category: Savage, G P.]]	+	[[Category: Savage, G P]]
-	[[Category: Smith, J A.]]	+	[[Category: Smith, J A]]
-	[[Category: Thienthong, N.]]	+	[[Category: Thienthong, N]]
-	[[Category: Vandergraaff, N.]]	+	[[Category: Vandergraaff, N]]
	[[Category: Aid]]		[[Category: Aid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:55, 1 August 2012

OCA — Wed, 01 Aug 2012 04:55:42 GMT

←Older revision		Revision as of 04:55, 1 August 2012
Line 1:		Line 1:
-	[[Image:3zso.~~jpg~~\|left\|200px]]	+	[[Image:3zso.png\|left\|200px]]

	{{STRUCTURE_3zso\| PDB=3zso \| SCENE= }}		{{STRUCTURE_3zso\| PDB=3zso \| SCENE= }}
Line 5:		Line 5:
	===Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design===		===Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design===

		+	{{ABSTRACT_PUBMED_22808106}}

	==About this Structure==		==About this Structure==
	[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA].		[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022808106</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus]]		[[Category: Human immunodeficiency virus]]
-	[[Category: Coates, J.]]	+	[[Category: Coates, J A.V.]]
	[[Category: Deadman, J J.]]		[[Category: Deadman, J J.]]
	[[Category: Dolezal, O.]]		[[Category: Dolezal, O.]]
-	[[Category: Francis, C.]]	+	[[Category: Francis, C L.]]
-	[[Category: Jones, E.]]	+	[[Category: Jones, E D.]]
	[[Category: Le, G.]]		[[Category: Le, G.]]
	[[Category: Newman, J.]]		[[Category: Newman, J.]]
	[[Category: Peat, T S.]]		[[Category: Peat, T S.]]
-	[[Category: Rhodes, D.]]	+	[[Category: Rhodes, D I.]]
-	[[Category: Ryan, J.]]	+	[[Category: Ryan, J H.]]
-	[[Category: Savage, P.]]	+	[[Category: Savage, G P.]]
-	[[Category: Smith, J.]]	+	[[Category: Smith, J A.]]
	[[Category: Thienthong, N.]]		[[Category: Thienthong, N.]]
	[[Category: Vandergraaff, N.]]		[[Category: Vandergraaff, N.]]
	[[Category: Aid]]		[[Category: Aid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:20, 11 July 2012

OCA — Wed, 11 Jul 2012 08:20:35 GMT

←Older revision		Revision as of 08:20, 11 July 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3zso.jpg\|left\|200px]]

-	~~The entry~~ 3zso ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_3zso\| PDB=3zso \| SCENE= }}

-	~~Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, N., Dolezal, O., Ryan, J., Savage, P., Francis, C.~~	+	===Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design===

-	~~Description: Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and~~ structure ~~based design~~	+
		+	==About this Structure==
		+	[[3zso]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus Human immunodeficiency virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ZSO OCA].
		+	[[Category: Human immunodeficiency virus]]
		+	[[Category: Coates, J.]]
		+	[[Category: Deadman, J J.]]
		+	[[Category: Dolezal, O.]]
		+	[[Category: Francis, C.]]
		+	[[Category: Jones, E.]]
		+	[[Category: Le, G.]]
		+	[[Category: Newman, J.]]
		+	[[Category: Peat, T S.]]
		+	[[Category: Rhodes, D.]]
		+	[[Category: Ryan, J.]]
		+	[[Category: Savage, P.]]
		+	[[Category: Smith, J.]]
		+	[[Category: Thienthong, N.]]
		+	[[Category: Vandergraaff, N.]]
		+	[[Category: Aid]]
		+	[[Category: Transferase]]

OCA at 06:20, 20 July 2011

OCA — Wed, 20 Jul 2011 06:20:58 GMT

←Older revision		Revision as of 06:20, 20 July 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3zso is ON HOLD	+	The entry 3zso is ON HOLD until Paper Publication

	Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, N., Dolezal, O., Ryan, J., Savage, P., Francis, C.		Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, N., Dolezal, O., Ryan, J., Savage, P., Francis, C.

	Description: Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design		Description: Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design

OCA: Protected "3zso" [edit=sysop:move=sysop]

OCA — Wed, 06 Jul 2011 18:32:30 GMT

Protected "3zso" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:32, 6 July 2011

OCA: New page: '''Unreleased structure''' The entry 3zso is ON HOLD Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, ...

OCA — Wed, 06 Jul 2011 18:32:29 GMT

New page: '''Unreleased structure''' The entry 3zso is ON HOLD Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, ...

New page

'''Unreleased structure'''

The entry 3zso is ON HOLD

Authors: Peat, T.S., Newman, J., Rhodes, D., Deadman, J.J., Vandergraaff, N., Le, G., Jones, E., Smith, J., Coates, J., Thienthong, N., Dolezal, O., Ryan, J., Savage, P., Francis, C.

Description: Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based design