6ogs - Revision history

OCA at 07:10, 11 October 2023

2023-10-11T07:10:34Z

← Older revision		Revision as of 07:10, 11 October 2023
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	<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ogs]] is a 1 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=6OGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ogs]] is a 1 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=6OGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.27Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [https://pdbe.org/6ogs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [https://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs 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=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [https://pdbe.org/6ogs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [https://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/O38885_9HIV1 O38885_9HIV1]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aoki, M]]		[[Category: Aoki M]]
	[[Category: Aoki-Ogata, H]]		[[Category: Aoki-Ogata H]]
	[[Category: Bulut, H]]		[[Category: Bulut H]]
	[[Category: Ghosh~~, A K~~]]		[[Category: Ghosh AK]]
	[[Category: Hattori~~, S I~~]]		[[Category: Hattori SI]]
	[[Category: Hayashi, H]]		[[Category: Hayashi H]]
	[[Category: Mitsuya, H]]		[[Category: Mitsuya H]]
	~~[[Category: Inhibitor]]~~
	~~[[Category: Viral protein]]~~
	~~[[Category: Viral protein-inhibitor complex~~]]

OCA at 05:26, 28 April 2021

2021-04-28T05:26:30Z

← Older revision		Revision as of 05:26, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ogs]] is a 1 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=6OGS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ogs]] is a 1 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=6OGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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~~://proteopedia.org/fgij/fg.htm?mol=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [~~http~~://pdbe.org/6ogs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs 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=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [https://pdbe.org/6ogs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [https://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:23, 26 August 2020

2020-08-26T11:23:46Z

← Older revision		Revision as of 11:23, 26 August 2020
Line 3:		Line 3:
	<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>		<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ogs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OGS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ogs]] is a 1 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=6OGS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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://proteopedia.org/fgij/fg.htm?mol=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [http://pdbe.org/6ogs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [http://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs 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=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [http://pdbe.org/6ogs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [http://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			HIV-1 protease inhibitors (PIs), such as darunavir (DRV), are the key component of antiretroviral therapy. However, HIV-1 often acquires resistance to PIs. Here, seven novel PIs were synthesized, by introducing single atom changes such as an exchange of a sulfur to an oxygen, scission of a single bond in P2'-cyclopropylaminobenzothiazole (or -oxazole), and/or P1-benzene ring with fluorine scan of mono- or bis-fluorine atoms around DRV's scaffold. X-ray structural analyses of the PIs complexed with wild-type Protease (PRWT) and highly-multi-PI-resistance-associated PRDRV(R)P51 revealed that the PIs better adapt to structural plasticity in PR with resistance-associated amino acid substitutions by formation of optimal sulfur bond and adaptation of cyclopropyl ring in the S2'-subsite. Furthermore, these PIs displayed increased cell permeability and extreme anti-HIV-1 potency compared to DRV. Our work provides the basis for developing novel PIs with high potency against PI-resistant HIV-1 variants with a high genetic barrier.

			Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity.,Bulut H, Hattori SI, Aoki-Ogata H, Hayashi H, Das D, Aoki M, Davis DA, Rao KV, Nyalapatla PR, Ghosh AK, Mitsuya H Sci Rep. 2020 Jun 30;10(1):10664. doi: 10.1038/s41598-020-65993-z. PMID:32606378<ref>PMID:32606378</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6ogs" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:50, 8 April 2020

2020-04-08T06:50:32Z

← Older revision		Revision as of 06:50, 8 April 2020
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry 6ogs is ON HOLD until Paper Publication~~		==X-ray crystal structure of darunavir-resistant HIV-1 protease (P30) in complex with GRL-001==
			<StructureSection load='6ogs' size='340' side='right'caption='[[6ogs]], [[Resolution\|resolution]] 1.27Å' scene=''>
	~~Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[6ogs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OGS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6OGS FirstGlance]. <br>
	~~Description:~~ X-ray crystal structure of darunavir-resistant HIV-1 protease (P30) in complex with GRL-001		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=JDY:(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl+[(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3-fluorophenyl)-3-hydroxybutan-2-yl]carbamate'>JDY</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ogs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ogs OCA], [http://pdbe.org/6ogs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ogs RCSB], [http://www.ebi.ac.uk/pdbsum/6ogs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ogs ProSAT]</span></td></tr>
	[[~~Category~~: ~~Hayashi~~, H]]		</table>
	[[~~Category~~: ~~Ghosh~~, A.K]]		__TOC__
			</StructureSection>
			[[Category: Large Structures]]
	[[Category: Aoki, M]]		[[Category: Aoki, M]]
	~~[[Category: Hattori, S.I]]~~
	~~[[Category: Mitsuya, H]]~~
	[[Category: Aoki-Ogata, H]]		[[Category: Aoki-Ogata, H]]
	[[Category: Bulut, H]]		[[Category: Bulut, H]]
			[[Category: Ghosh, A K]]
			[[Category: Hattori, S I]]
			[[Category: Hayashi, H]]
			[[Category: Mitsuya, H]]
			[[Category: Inhibitor]]
			[[Category: Viral protein]]
			[[Category: Viral protein-inhibitor complex]]

OCA at 04:54, 24 April 2019

2019-04-24T04:54:11Z

← Older revision		Revision as of 04:54, 24 April 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6ogs is ON HOLD		The entry 6ogs is ON HOLD until Paper Publication

	Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.		Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.

OCA: Protected "6ogs" [edit=sysop:move=sysop]

2019-04-10T05:35:32Z

Protected "6ogs" [edit=sysop:move=sysop]

← Older revision	Revision as of 05:35, 10 April 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6ogs is ON HOLD Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H. Description: X-ray crystal struc...

2019-04-10T05:35:30Z

New page: '''Unreleased structure''' The entry 6ogs is ON HOLD Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H. Description: X-ray crystal struc...

New page

'''Unreleased structure'''

The entry 6ogs is ON HOLD

Authors: Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.

Description: X-ray crystal structure of darunavir-resistant HIV-1 protease (P30) in complex with GRL-001
[[Category: Unreleased Structures]]
[[Category: Hayashi, H]]
[[Category: Ghosh, A.K]]
[[Category: Aoki, M]]
[[Category: Hattori, S.I]]
[[Category: Mitsuya, H]]
[[Category: Aoki-Ogata, H]]
[[Category: Bulut, H]]