6dpy - Revision history

OCA at 06:12, 11 October 2023

2023-10-11T06:12:26Z

← Older revision		Revision as of 06:12, 11 October 2023
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	==X-ray crystal structure of AmpC beta-lactamase with inhibitor==		==X-ray crystal structure of AmpC beta-lactamase with inhibitor==
	<StructureSection load='6dpy' size='340' side='right' caption='[[6dpy]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='6dpy' size='340' side='right'caption='[[6dpy]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dpy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dpy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DPY FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=H7A:4~~-{[~~(4R)-6-fluoro-3,4-dihydro-2H-~~1~~-benzopyran-4-yl]sulfamoyl}-2,5-dimethylfuran-3-carboxylic+acid'>H7A</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]] 1.91Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ampC, ampA, b4150, JW4111 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~83333 ECOLI])</td~~><~~/tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H7A:4-{[(4R)-6-fluoro-3,4-dihydro-2H-1-benzopyran-4-yl]sulfamoyl}-2,5-dimethylfuran-3-carboxylic+acid'>H7A</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/Beta~~-~~lactamase Beta~~-~~lactamase~~], ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~3~~.5.2.6 3.5.2.6]~~ </~~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=6dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpy OCA], [https://pdbe.org/6dpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dpy RCSB], [https://www.ebi.ac.uk/pdbsum/6dpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpy 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=6dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpy OCA], [~~http~~://pdbe.org/6dpy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dpy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dpy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.		[https://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6dpy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dpy" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Beta-lactamase 3D structures\|Beta-lactamase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Beta~~-~~lactamase~~]]		[[Category: Escherichia coli K-12]]
	[[Category: ~~Ecoli~~]]		[[Category: Large Structures]]
	[[Category: Singh, I]]		[[Category: Singh I]]
	~~[[Category: Ampc beta-lacatamase]]~~
	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~
	~~[[Category: Inhibitor complex~~]]

OCA at 15:56, 27 February 2019

2019-02-27T15:56:00Z

← Older revision		Revision as of 15:56, 27 February 2019
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	<StructureSection load='6dpy' size='340' side='right' caption='[[6dpy]], [[Resolution\|resolution]] 1.91Å' scene=''>		<StructureSection load='6dpy' size='340' side='right' caption='[[6dpy]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dpy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dpy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H7A:4-{[(4R)-6-fluoro-3,4-dihydro-2H-1-benzopyran-4-yl]sulfamoyl}-2,5-dimethylfuran-3-carboxylic+acid'>H7A</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H7A:4-{[(4R)-6-fluoro-3,4-dihydro-2H-1-benzopyran-4-yl]sulfamoyl}-2,5-dimethylfuran-3-carboxylic+acid'>H7A</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ampC, ampA, b4150, JW4111 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=6dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpy OCA], [http://pdbe.org/6dpy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpy RCSB], [http://www.ebi.ac.uk/pdbsum/6dpy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpy 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=6dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpy OCA], [http://pdbe.org/6dpy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpy RCSB], [http://www.ebi.ac.uk/pdbsum/6dpy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpy ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.		[[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Despite intense interest in expanding chemical space, libraries containing hundreds-of-millions to billions of diverse molecules have remained inaccessible. Here we investigate structure-based docking of 170 million make-on-demand compounds from 130 well-characterized reactions. The resulting library is diverse, representing over 10.7 million scaffolds that are otherwise unavailable. For each compound in the library, docking against AmpC beta-lactamase (AmpC) and the D4 dopamine receptor were simulated. From the top-ranking molecules, 44 and 549 compounds were synthesized and tested for interactions with AmpC and the D4 dopamine receptor, respectively. We found a phenolate inhibitor of AmpC, which revealed a group of inhibitors without known precedent. This molecule was optimized to 77 nM, which places it among the most potent non-covalent AmpC inhibitors known. Crystal structures of this and other AmpC inhibitors confirmed the docking predictions. Against the D4 dopamine receptor, hit rates fell almost monotonically with docking score, and a hit-rate versus score curve predicted that the library contained 453,000 ligands for the D4 dopamine receptor. Of 81 new chemotypes discovered, 30 showed submicromolar activity, including a 180-pM subtype-selective agonist of the D4 dopamine receptor.

			Ultra-large library docking for discovering new chemotypes.,Lyu J, Wang S, Balius TE, Singh I, Levit A, Moroz YS, O'Meara MJ, Che T, Algaa E, Tolmachova K, Tolmachev AA, Shoichet BK, Roth BL, Irwin JJ Nature. 2019 Feb;566(7743):224-229. doi: 10.1038/s41586-019-0917-9. Epub 2019 Feb, 6. PMID:30728502<ref>PMID:30728502</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6dpy" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Beta-lactamase]]		[[Category: Beta-lactamase]]
			[[Category: Ecoli]]
	[[Category: Singh, I]]		[[Category: Singh, I]]
	[[Category: Ampc beta-lacatamase]]		[[Category: Ampc beta-lacatamase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Inhibitor complex]]		[[Category: Inhibitor complex]]

OCA at 07:17, 4 July 2018

2018-07-04T07:17:31Z

← Older revision		Revision as of 07:17, 4 July 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6dpy is ~~ON HOLD until Paper Publication~~		==X-ray crystal structure of AmpC beta-lactamase with inhibitor==
			<StructureSection load='6dpy' size='340' side='right' caption='[[6dpy]], [[Resolution\|resolution]] 1.91Å' scene=''>
	~~Authors~~: ~~Singh~~, I.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6dpy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DPY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DPY FirstGlance]. <br>
	~~Description~~: ~~X-ray crystal structure of AmpC~~ beta-lactamase with ~~inhibitor~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H7A:4-{[(4R)-6-fluoro-3,4-dihydro-2H-1-benzopyran-4-yl]sulfamoyl}-2,5-dimethylfuran-3-carboxylic+acid'>H7A</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=6dpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dpy OCA], [http://pdbe.org/6dpy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dpy RCSB], [http://www.ebi.ac.uk/pdbsum/6dpy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dpy ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI]] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
			__TOC__
			</StructureSection>
			[[Category: Beta-lactamase]]
	[[Category: Singh, I]]		[[Category: Singh, I]]
			[[Category: Ampc beta-lacatamase]]
			[[Category: Hydrolase-hydrolase inhibitor complex]]
			[[Category: Inhibitor complex]]

OCA at 04:00, 27 June 2018

2018-06-27T04:00:38Z

← Older revision		Revision as of 04:00, 27 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Singh, I.		Authors: Singh, I.

	Description: X-ray crystal structure of AmpC beta-lactamase with ~~nanomolar~~ inhibitor		Description: X-ray crystal structure of AmpC beta-lactamase with inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Singh, I]]		[[Category: Singh, I]]

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

2018-06-20T04:06:46Z

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

← Older revision	Revision as of 04:06, 20 June 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6dpy is ON HOLD Authors: Singh, I. Description: X-ray crystal structure of AmpC beta-lactamase with nanomolar inhibitor [[Category: Unreleased Stru...

2018-06-20T04:06:44Z

New page: '''Unreleased structure''' The entry 6dpy is ON HOLD Authors: Singh, I. Description: X-ray crystal structure of AmpC beta-lactamase with nanomolar inhibitor [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 6dpy is ON HOLD

Authors: Singh, I.

Description: X-ray crystal structure of AmpC beta-lactamase with nanomolar inhibitor
[[Category: Unreleased Structures]]
[[Category: Singh, I]]