2i0d - Revision history

OCA at 10:04, 30 August 2023

2023-08-30T10:04:20Z

←Older revision		Revision as of 10:04, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2i0d' size='340' side='right'caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2i0d' size='340' side='right'caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I0D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ioa\|2ioa]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [https://pdbe.org/2i0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [https://www.ebi.ac.uk/pdbsum/2i0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i0d 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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [https://pdbe.org/2i0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [https://www.ebi.ac.uk/pdbsum/2i0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i0d ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O38731_9HIV1 O38731_9HIV1]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ali, A]]	+	[[Category: Ali A]]
-	[[Category: Anjum~~, S G~~]]	+	[[Category: Anjum SG]]
-	[[Category: Cao, H]]	+	[[Category: Cao H]]
-	[[Category: Nalam~~, M N.L~~]]	+	[[Category: Nalam MNL]]
-	[[Category: Rana~~, T M~~]]	+	[[Category: Rana TM]]
-	[[Category: Reddy~~, K K~~]]	+	[[Category: Reddy KK]]
-	[[Category: Schiffer~~, C A]]~~	+	[[Category: Schiffer CA]]
-	~~[[Category: Drug design]]~~	+
-	~~[[Category: Hiv-1 protease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protease inhibitor~~]]	+

OCA at 07:25, 24 March 2021

2021-03-24T07:25:56Z

←Older revision		Revision as of 07:25, 24 March 2021
Line 1:		Line 1:

	==Crystal structure of AD-81 complexed with wild type HIV-1 protease==		==Crystal structure of AD-81 complexed with wild type HIV-1 protease==
-	<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2i0d' size='340' side='right'caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2I0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I0D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ioa\|2ioa]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [~~http~~://pdbe.org/2i0d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2i0d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2i0d 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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [https://pdbe.org/2i0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [https://www.ebi.ac.uk/pdbsum/2i0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i0d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/2i0d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/2i0d_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]	+	*[[Immunodeficiency virus protease 3D structures\|Immunodeficiency virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ali, A]]		[[Category: Ali, A]]
	[[Category: Anjum, S G]]		[[Category: Anjum, S G]]

OCA at 08:21, 18 October 2017

2017-10-18T08:21:13Z

←Older revision		Revision as of 08:21, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of AD-81 complexed with wild type HIV-1 protease==		==Crystal structure of AD-81 complexed with wild type HIV-1 protease==
	<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://pdbe.org/2i0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d 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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://pdbe.org/2i0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2i0d ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2i0d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2i0d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Immunodeficiency virus protease\|Immunodeficiency virus protease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:21, 8 February 2016

2016-02-08T17:21:49Z

←Older revision		Revision as of 17:21, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2i0d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:46, 10 September 2015

2015-09-10T13:46:49Z

←Older revision		Revision as of 13:46, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_1 Human immunodeficiency virus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 ~~Human immunodeficiency virus 1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d 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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://pdbe.org/2i0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2i0d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Human immunodeficiency virus 1]]
	[[Category: Ali, A]]		[[Category: Ali, A]]
	[[Category: Anjum, S G]]		[[Category: Anjum, S G]]

OCA at 08:35, 16 January 2015

2015-01-16T08:35:05Z

←Older revision		Revision as of 08:35, 16 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I0D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d 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=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Ali, A.]]	+	[[Category: Ali, A]]
-	[[Category: Anjum, S G.]]	+	[[Category: Anjum, S G]]
-	[[Category: Cao, H.]]	+	[[Category: Cao, H]]
-	[[Category: Nalam, M N.L.]]	+	[[Category: Nalam, M N.L]]
-	[[Category: Rana, T M.]]	+	[[Category: Rana, T M]]
-	[[Category: Reddy, K K.]]	+	[[Category: Reddy, K K]]
-	[[Category: Schiffer, C A.]]	+	[[Category: Schiffer, C A]]
	[[Category: Drug design]]		[[Category: Drug design]]
	[[Category: Hiv-1 protease]]		[[Category: Hiv-1 protease]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Protease inhibitor]]		[[Category: Protease inhibitor]]

OCA at 08:13, 30 September 2014

2014-09-30T08:13:37Z

←Older revision		Revision as of 08:13, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2i0d.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of AD-81 complexed with wild type HIV-1 protease==
		+	<StructureSection load='2i0d' size='340' side='right' caption='[[2i0d]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2I0D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MUT:(5S)-3-(3-ACETYLPHENYL)-N-[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]-2-OXO-1,3-OXAZOLIDINE-5-CARBOXAMIDE'>MUT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ioa\|2ioa]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 Human immunodeficiency virus 1])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2i0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2i0d RCSB], [http://www.ebi.ac.uk/pdbsum/2i0d PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/2i0d_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here, we describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors incorporating N-phenyloxazolidinone-5-carboxamides into the (hydroxyethylamino)sulfonamide scaffold as P2 ligands. Series of inhibitors with variations at the P2 phenyloxazolidinone and the P2' phenylsulfonamide moieties were synthesized. Compounds with the (S)-enantiomer of substituted phenyloxazolidinones at P2 show highly potent inhibitory activities against HIV-1 protease. The inhibitors possessing 3-acetyl, 4-acetyl, and 3-trifluoromethyl groups at the phenyl ring of the oxazolidinone fragment are the most potent in each series, with K(i) values in the low picomolar (pM) range. The electron-donating groups 4-methoxy and 1,3-dioxolane are preferred at P2' phenyl ring, as compounds with other substitutions show lower binding affinities. Attempts to replace the isobutyl group at P1' with small cyclic moieties caused significant loss of affinities in the resulting compounds. Crystal structure analysis of the two most potent inhibitors in complex with the HIV-1 protease provided valuable information on the interactions between the inhibitor and the protease enzyme. In both inhibitor - enzyme complexes, the carbonyl group of the oxazolidinone ring makes hydrogenbond interactions with relatively conserved Asp29 residue of the protease. Potent inhibitors from each series incorporating various phenyloxazolidinone based P2 ligands were selected and their activities against a panel of multidrug-resistant (MDR) protease variants were determined. Interestingly, the most potent protease inhibitor starts out with extremely tight affinity for the wild-type enzyme (K(i) = 0.8 pM), and even against the MDR variants it retains picomolar to low nanomolar K(i), which is highly comparable with the best FDA-approved protease inhibitors.

-	~~{{STRUCTURE_2i0d\| PDB=2i0d \| SCENE= }}~~	+	Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands.,Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM J Med Chem. 2006 Dec 14;49(25):7342-56. PMID:17149864<ref>PMID:17149864</ref>

-	~~===Crystal structure~~ of ~~AD-81 complexed with wild type HIV-1 protease===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17149864}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2i0d]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017149864<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Ali, A.]]		[[Category: Ali, A.]]

OCA: Protected "2i0d" [edit=sysop:move=sysop]

2013-01-07T13:16:50Z

Protected "2i0d" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:16, 7 January 2013

OCA at 13:16, 7 January 2013

2013-01-07T13:16:49Z

←Older revision		Revision as of 13:16, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2i0d.png\|left\|200px]]		[[Image:2i0d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2i0d", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2i0d\| PDB=2i0d \| SCENE= }}		{{STRUCTURE_2i0d\| PDB=2i0d \| SCENE= }}

	===Crystal structure of AD-81 complexed with wild type HIV-1 protease===		===Crystal structure of AD-81 complexed with wild type HIV-1 protease===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17149864}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17149864 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17149864}}		{{ABSTRACT_PUBMED_17149864}}

	==About this Structure==		==About this Structure==
-	~~2I0D~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA].	+	[[2i0d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17149864~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017149864</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Ali, A.]]		[[Category: Ali, A.]]
Line 34:		Line 22:
	[[Category: Drug design]]		[[Category: Drug design]]
	[[Category: Hiv-1 protease]]		[[Category: Hiv-1 protease]]
		+	[[Category: Hydrolase]]
	[[Category: Protease inhibitor]]		[[Category: Protease inhibitor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:45:14 2009''

OCA at 22:45, 16 February 2009

2009-02-16T22:45:15Z

←Older revision		Revision as of 22:45, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2I0D is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA].	+	2I0D is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I0D OCA].

	==Reference==		==Reference==
-	Discovery of HIV-1 protease inhibitors with picomolar affinities incorporating N-aryl-oxazolidinone-5-carboxamides as novel P2 ligands., Ali A, Reddy GS, Cao H, Anjum SG, Nalam MN, Schiffer CA, Rana TM, J Med Chem. 2006 Dec 14;49(25):7342-56. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17149864 17149864]~~	+	<ref group="xtra">PMID:17149864</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
-	[[Category: Single protein]]
	[[Category: Ali, A.]]		[[Category: Ali, A.]]
	[[Category: Anjum, S G.]]		[[Category: Anjum, S G.]]
Line 37:		Line 36:
	[[Category: Protease inhibitor]]		[[Category: Protease inhibitor]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 05~~:14:~~11 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:45:14 2009''