5u6e - Revision history

OCA at 13:21, 4 October 2023

OCA — Wed, 04 Oct 2023 13:21:45 GMT

←Older revision		Revision as of 13:21, 4 October 2023
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	<StructureSection load='5u6e' size='340' side='right'caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5u6e' size='340' side='right'caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u6e]] 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=5U6E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u6e]] 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=5U6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U6E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82M:N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE'>82M</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.095Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=82M:N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE'>82M</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=5u6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6e OCA], [~~http~~://pdbe.org/5u6e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u6e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u6e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6e 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=5u6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6e OCA], [https://pdbe.org/5u6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u6e RCSB], [https://www.ebi.ac.uk/pdbsum/5u6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6e ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Debnath~~, A K~~]]	+	[[Category: Debnath AK]]
-	[[Category: Kwon~~, Y D~~]]	+	[[Category: Kwon YD]]
-	[[Category: Kwong~~, P D]]~~	+	[[Category: Kwong PD]]
-	~~[[Category: Hiv-1]]~~	+
-	~~[[Category: Nbd-14010]]~~	+
-	~~[[Category: Small molecule]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virus entry antagonist~~]]	+

OCA at 09:28, 4 December 2019

OCA — Wed, 04 Dec 2019 09:28:12 GMT

←Older revision		Revision as of 09:28, 4 December 2019
Line 1:		Line 1:

	==Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010==		==Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010==
-	<StructureSection load='5u6e' size='340' side='right' caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5u6e' size='340' side='right'caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5u6e]] 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=5U6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6E FirstGlance]. <br>		<table><tr><td colspan='2'>[[5u6e]] 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=5U6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6E FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5u6e" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5u6e" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Gp120 3D structures\|Gp120 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Debnath, A K]]		[[Category: Debnath, A K]]
	[[Category: Kwon, Y D]]		[[Category: Kwon, Y D]]

OCA at 23:26, 15 November 2017

OCA — Wed, 15 Nov 2017 23:26:03 GMT

←Older revision		Revision as of 23:26, 15 November 2017
Line 3:		Line 3:
	<StructureSection load='5u6e' size='340' side='right' caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5u6e' size='340' side='right' caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u6e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u6e]] 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=5U6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82M:N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE'>82M</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82M:N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE'>82M</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIV-1 Env ([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=5u6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6e OCA], [http://pdbe.org/5u6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6e RCSB], [http://www.ebi.ac.uk/pdbsum/5u6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6e ProSAT]</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=5u6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6e OCA], [http://pdbe.org/5u6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6e RCSB], [http://www.ebi.ac.uk/pdbsum/5u6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6e ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:39, 27 April 2017

OCA — Thu, 27 Apr 2017 07:39:00 GMT

←Older revision		Revision as of 07:39, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u6e is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010==
		+	<StructureSection load='5u6e' size='340' side='right' caption='[[5u6e]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5u6e]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U6E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U6E FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=82M:N-{(1S)-2-AMINO-1-[5-(HYDROXYMETHYL)-4-METHYL-1,3-THIAZOL-2-YL]ETHYL}-5-(4-CHLORO-3-FLUOROPHENYL)-1H-PYRROLE-2-CARBOXAMIDE'>82M</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=5u6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u6e OCA], [http://pdbe.org/5u6e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u6e RCSB], [http://www.ebi.ac.uk/pdbsum/5u6e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u6e ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In our attempt to optimize the lead HIV-1 entry antagonist, NBD-11021, we present in this study the rational design and synthesis of 60 new analogues and determination of their antiviral activity in a single-cycle and a multicycle infection assay to derive a comprehensive structure-activity relationship (SAR). Two of these compounds, NBD-14088 and NBD-14107, showed significant improvement in antiviral activity compared to the lead entry antagonist in a single-cycle assay against a large panel of Env-pseudotyped viruses. The X-ray structure of a similar compound, NBD-14010, confirmed the binding mode of the newly designed compounds. The in vitro ADMET profiles of these compounds are comparable to that of the most potent attachment inhibitor BMS-626529, a prodrug of which is currently undergoing phase III clinical trials. The systematic study presented here is expected to pave the way for improving the potency, toxicity, and ADMET profile of this series of compounds with the potential to be moved to the early preclinical development.

-	~~Authors: Kwon~~, ~~Y.D~~., ~~Debnath~~, A~~.K.~~, Kwong, P.D.	+	Synthesis, Antiviral Potency, in Vitro ADMET, and X-ray Structure of Potent CD4 Mimics as Entry Inhibitors That Target the Phe43 Cavity of HIV-1 gp120.,Curreli F, Kwon YD, Belov DS, Ramesh RR, Kurkin AV, Altieri A, Kwong PD, Debnath AK J Med Chem. 2017 Mar 16. doi: 10.1021/acs.jmedchem.7b00179. PMID:28266845<ref>PMID:28266845</ref>

-	~~Description: Crystal structure~~ of ~~clade A~~/~~E HIV~~-~~1 gp120 core in complex with NBD~~-~~14010~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Debnath, A.K]]	+	<div class="pdbe-citations 5u6e" style="background-color:#fffaf0;"></div>
-	[[Category: Kwon, Y.D]]	+	== References ==
-	[[Category: Kwong, P.D]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Debnath, A K]]
		+	[[Category: Kwon, Y D]]
		+	[[Category: Kwong, P D]]
		+	[[Category: Hiv-1]]
		+	[[Category: Nbd-14010]]
		+	[[Category: Small molecule]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus entry antagonist]]

OCA at 14:12, 9 March 2017

OCA — Thu, 09 Mar 2017 14:12:22 GMT

←Older revision		Revision as of 14:12, 9 March 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5u6e is ON HOLD	+	The entry 5u6e is ON HOLD until Paper Publication

	Authors: Kwon, Y.D., Debnath, A.K., Kwong, P.D.		Authors: Kwon, Y.D., Debnath, A.K., Kwong, P.D.

OCA at 15:07, 2 January 2017

OCA — Mon, 02 Jan 2017 15:07:08 GMT

←Older revision		Revision as of 15:07, 2 January 2017
Line 3:		Line 3:
	The entry 5u6e is ON HOLD		The entry 5u6e is ON HOLD

-	Authors: Kwon, Y.D., Debnath, A.K., Kwong, P. D.	+	Authors: Kwon, Y.D., Debnath, A.K., Kwong, P.D.

	Description: Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010		Description: Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010
Line 9:		Line 9:
	[[Category: Debnath, A.K]]		[[Category: Debnath, A.K]]
	[[Category: Kwon, Y.D]]		[[Category: Kwon, Y.D]]
-	[[Category: Kwong, P. D]]	+	[[Category: Kwong, P.D]]

OCA: Protected "5u6e" [edit=sysop:move=sysop]

OCA — Thu, 15 Dec 2016 17:44:41 GMT

Protected "5u6e" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:44, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u6e is ON HOLD Authors: Kwon, Y.D., Debnath, A.K., Kwong, P. D. Description: Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-1...

OCA — Thu, 15 Dec 2016 17:44:40 GMT

New page: '''Unreleased structure''' The entry 5u6e is ON HOLD Authors: Kwon, Y.D., Debnath, A.K., Kwong, P. D. Description: Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-1...

New page

'''Unreleased structure'''

The entry 5u6e is ON HOLD

Authors: Kwon, Y.D., Debnath, A.K., Kwong, P. D.

Description: Crystal structure of clade A/E HIV-1 gp120 core in complex with NBD-14010
[[Category: Unreleased Structures]]
[[Category: Debnath, A.K]]
[[Category: Kwon, Y.D]]
[[Category: Kwong, P. D]]