4dvs - Revision history

OCA at 02:48, 21 November 2024

2024-11-21T02:48:26Z

← Older revision		Revision as of 02:48, 21 November 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]		[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.

			Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.,Kwon YD, Lalonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB 3rd, Debnath AK, Kwong PD PLoS One. 2014 Jan 28;9(1):e85940. doi: 10.1371/journal.pone.0085940. eCollection, 2014. PMID:24489681<ref>PMID:24489681</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 4dvs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Gp120 3D structures\|Gp120 3D structures]]		*[[Gp120 3D structures\|Gp120 3D structures]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:45, 14 March 2024

2024-03-14T14:45:58Z

← Older revision		Revision as of 14:45, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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]] 2.1Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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'>[https://proteopedia.org/fgij/fg.htm?mol=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [https://pdbe.org/4dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [https://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [https://pdbe.org/4dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [https://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]]		[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.

	Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.,Kwon YD, Lalonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB 3rd, Debnath AK, Kwong PD PLoS One. 2014 Jan 28;9(1):e85940. doi: 10.1371/journal.pone.0085940. eCollection, 2014. PMID:24489681<ref>PMID:24489681</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4dvs" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Gp120 3D structures\|Gp120 3D structures]]		*[[Gp120 3D structures\|Gp120 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:40, 21 September 2022

2022-09-21T08:40:36Z

← Older revision		Revision as of 08:40, 21 September 2022
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	<StructureSection load='4dvs' size='340' side='right'caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4dvs' size='340' side='right'caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dvs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DVS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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" id="ligandDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]~~</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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [https://pdbe.org/4dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [https://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [~~http~~://pdbe.org/4dvs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs 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 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kwon~~, Y D~~]]		[[Category: Kwon YD]]
	[[Category: Kwong~~, P D]]~~		[[Category: Kwong PD]]
	~~[[Category: Cd4 binding site]]~~
	~~[[Category: Hiv-1 gp120]]~~
	~~[[Category: Nbd-557]]~~
	~~[[Category: Small molecule inhibitor]]~~
	~~[[Category: Viral protein-transcription inhibitor complex~~]]

OCA at 16:46, 28 August 2019

2019-08-28T16:46:07Z

← Older revision		Revision as of 16:46, 28 August 2019
Line 1:		Line 1:

	==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==		==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==
	<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4dvs' size='340' side='right'caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dvs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dvs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 4dvs" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4dvs" 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: Kwon, Y D]]		[[Category: Kwon, Y D]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]

OCA at 11:28, 3 August 2017

2017-08-03T11:28:31Z

← Older revision		Revision as of 11:28, 3 August 2017
Line 3:		Line 3:
	<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>		<table><tr><td colspan='2'>[[4dvs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env, 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://pdbe.org/4dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://pdbe.org/4dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	[[http://www.uniprot.org/uniprot/Q0ED31_9HIV1 Q0ED31_9HIV1]] The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface (By similarity).[RuleBase:RU004292][SAAS:SAAS000328_004_020447] The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Kwon,Y D]]		[[Category: Kwon, Y D]]
	[[Category: Kwong, P D]]		[[Category: Kwong, P D]]
	[[Category: Cd4 binding site]]		[[Category: Cd4 binding site]]

OCA at 20:35, 5 August 2016

2016-08-05T20:35:45Z

← Older revision		Revision as of 20:35, 5 August 2016
Line 1:		Line 1:

	==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==		==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==
	<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env, HIV-1 Env ([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">env, 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://pdbe.org/4dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 4dvs" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:42, 25 December 2014

2014-12-25T21:42:22Z

← Older revision		Revision as of 21:42, 25 December 2014
Line 8:		Line 8:
	<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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q0ED31_9HIV1 Q0ED31_9HIV1]] The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface (By similarity).[RuleBase:RU004292][SAAS:SAAS000328_004_020447] The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:11, 17 December 2014

2014-12-17T09:11:36Z

← Older revision		Revision as of 09:11, 17 December 2014
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	~~{{STRUCTURE_4dvs\| PDB=4dvs \| SCENE= }}~~		==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==
	===Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557===		<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution\|resolution]] 2.10Å' scene=''>
	~~{{ABSTRACT_PUBMED_24489681}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4dvr\|4dvr]], [[4dvt\|4dvt]], [[4dvu\|4dvu]], [[4dvv\|4dvv]], [[4dvw\|4dvw]], [[4dvx\|4dvx]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">env, 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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.

	~~==Function==~~		Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.,Kwon YD, Lalonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB 3rd, Debnath AK, Kwong PD PLoS One. 2014 Jan 28;9(1):e85940. doi: 10.1371/journal.pone.0085940. eCollection, 2014. PMID:24489681<ref>PMID:24489681</ref>
	~~[[http://www.uniprot.org/uniprot/Q0ED31_9HIV1 Q0ED31_9HIV1]] The envelope glyprotein gp160 precursor down~~-~~modulates cell surface CD4 antigen by interacting~~ with ~~it in~~ the ~~endoplasmic reticulum and blocking its transport to the cell surface~~ (~~By similarity~~).~~[RuleBase~~:RU004292][SAAS:SAAS000328_004_020447] The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. ~~Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells~~. ~~Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells~~. ~~This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity)~~.

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[4dvs]] 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=4DVS OCA].~~		</div>
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:024489681</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
	~~[[Category: 9hiv1]]~~		</StructureSection>
	[[Category: Kwon,Y D.]]		[[Category: Kwon,Y D]]
	[[Category: Kwong, P D.]]		[[Category: Kwong, P D]]
	[[Category: Cd4 binding site]]		[[Category: Cd4 binding site]]
	[[Category: Hiv-1 gp120]]		[[Category: Hiv-1 gp120]]

OCA at 09:11, 19 March 2014

2014-03-19T09:11:53Z

← Older revision		Revision as of 09:11, 19 March 2014
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	~~[[Image:4dvs.jpg\|left\|200px]]~~

	{{STRUCTURE_4dvs\| PDB=4dvs \| SCENE= }}		{{STRUCTURE_4dvs\| PDB=4dvs \| SCENE= }}

	===Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557===		===Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557===
			{{ABSTRACT_PUBMED_24489681}}

			==Function==
			[[http://www.uniprot.org/uniprot/Q0ED31_9HIV1 Q0ED31_9HIV1]] The envelope glyprotein gp160 precursor down-modulates cell surface CD4 antigen by interacting with it in the endoplasmic reticulum and blocking its transport to the cell surface (By similarity).[RuleBase:RU004292][SAAS:SAAS000328_004_020447] The gp120-gp41 heterodimer allows rapid transcytosis of the virus through CD4 negative cells such as simple epithelial monolayers of the intestinal, rectal and endocervical epithelial barriers. Both gp120 and gp41 specifically recognize glycosphingolipids galactosyl-ceramide (GalCer) or 3' sulfo-galactosyl-ceramide (GalS) present in the lipid rafts structures of epithelial cells. Binding to these alternative receptors allows the rapid transcytosis of the virus through the epithelial cells. This transcytotic vesicle-mediated transport of virions from the apical side to the basolateral side of the epithelial cells does not involve infection of the cells themselves (By similarity).

	==About this Structure==		==About this Structure==
	[[4dvs]] 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=4DVS OCA].		[[4dvs]] 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=4DVS OCA].
	[[Category: ~~Human immunodeficiency virus 1~~]]
			==Reference==
			<ref group="xtra">PMID:024489681</ref><references group="xtra"/><references/>
			[[Category: 9hiv1]]
	[[Category: Kwon,Y D.]]		[[Category: Kwon,Y D.]]
	[[Category: Kwong, P D.]]		[[Category: Kwong, P D.]]

OCA at 14:55, 27 February 2013

2013-02-27T14:55:28Z

← Older revision		Revision as of 14:55, 27 February 2013
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	~~'''Unreleased structure'''~~		[[Image:4dvs.jpg\|left\|200px]]

	~~The entry~~ 4dvs ~~is ON HOLD~~ ~~until Feb 27 2014~~		{{STRUCTURE_4dvs\| PDB=4dvs \| SCENE= }}

	~~Authors: Kwon,Y.D., Kwong, P.D.~~		===Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557===

	~~Description~~: ~~Crystal structure of clade A~~/~~E 93TH057 HIV~~-1 gp120 ~~core in complex with NBD~~-557
			==About this Structure==
			[[4dvs]] 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=4DVS OCA].
			[[Category: Human immunodeficiency virus 1]]
			[[Category: Kwon,Y D.]]
			[[Category: Kwong, P D.]]
			[[Category: Cd4 binding site]]
			[[Category: Hiv-1 gp120]]
			[[Category: Nbd-557]]
			[[Category: Small molecule inhibitor]]
			[[Category: Viral protein-transcription inhibitor complex]]