7rgj - Revision history

OCA at 16:31, 18 October 2023

OCA — Wed, 18 Oct 2023 16:31:10 GMT

←Older revision		Revision as of 16:31, 18 October 2023
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	==DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)==		==DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)==
-	<StructureSection load='7rgj' size='340' side='right'caption='[[7rgj]]' scene=''>	+	<StructureSection load='7rgj' size='340' side='right'caption='[[7rgj]], [[Resolution\|resolution]] 1.44Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RGJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rgj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RGJ FirstGlance]. <br>
-	</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=7rgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rgj OCA], [https://pdbe.org/7rgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rgj RCSB], [https://www.ebi.ac.uk/pdbsum/7rgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rgj ProSAT]</span></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]] 1.44Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=560:5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine'>560</scene>, <scene name='pdbligand=8MU:5-[(3S)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine'>8MU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=7rgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rgj OCA], [https://pdbe.org/7rgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rgj RCSB], [https://www.ebi.ac.uk/pdbsum/7rgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rgj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DYR1_ECOLX DYR1_ECOLX] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Two plasmid-encoded dihydrofolate reductase (DHFR) isoforms, DfrA1 and DfrA5, that give rise to high levels of resistance in Gram-negative bacteria were structurally and biochemically characterized to reveal the mechanism of TMP resistance and to support phylogenic groupings for drug development against antibiotic resistant pathogens. Preliminary screening of novel antifolates revealed related chemotypes that showed high levels of inhibitory potency against Escherichia coli chromosomal DHFR (EcDHFR), DfrA1, and DfrA5. Kinetics and biophysical analysis, coupled with crystal structures of trimethoprim bound to EcDHFR, DfrA1 and DfrA5, and two propargyl-linked antifolates (PLA) complexed with EcDHFR, DfrA1 and DfrA5, were determined to define structural features of the substrate binding pocket and guide synthesis of pan-DHFR inhibitors.
		+
		+	Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens.,Krucinska J, Lombardo MN, Erlandsen H, Estrada A, Si D, Viswanathan K, Wright DL Commun Biol. 2022 May 13;5(1):459. doi: 10.1038/s42003-022-03384-y. PMID:35562546<ref>PMID:35562546</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7rgj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lombardo MN]]		[[Category: Lombardo MN]]
	[[Category: Wright DL]]		[[Category: Wright DL]]

OCA at 07:58, 25 May 2022

OCA — Wed, 25 May 2022 07:58:45 GMT

←Older revision		Revision as of 07:58, 25 May 2022
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-	'''Unreleased structure'''

-	~~The entry 7rgj is ON HOLD until Paper Publication~~	+	==DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)==
-		+	<StructureSection load='7rgj' size='340' side='right'caption='[[7rgj]]' scene=''>
-	~~Authors: Lombardo, M.N., Wright, D.L.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RGJ FirstGlance]. <br>
-	~~Description:~~ DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)	+	</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=7rgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rgj OCA], [https://pdbe.org/7rgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rgj RCSB], [https://www.ebi.ac.uk/pdbsum/7rgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rgj ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Wright~~, D.L]]	+	__TOC__
-	[[Category: Lombardo~~, M.N~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lombardo MN]]
		+	[[Category: Wright DL]]

OCA at 07:42, 29 September 2021

OCA — Wed, 29 Sep 2021 07:42:23 GMT

←Older revision		Revision as of 07:42, 29 September 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7rgj is ON HOLD until ~~sometime in the future~~	+	The entry 7rgj is ON HOLD until Paper Publication

	Authors: Lombardo, M.N., Wright, D.L.		Authors: Lombardo, M.N., Wright, D.L.
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	Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)		Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Lombardo, M.N]]
	[[Category: Wright, D.L]]		[[Category: Wright, D.L]]
		+	[[Category: Lombardo, M.N]]

OCA at 07:39, 8 September 2021

OCA — Wed, 08 Sep 2021 07:39:38 GMT

←Older revision		Revision as of 07:39, 8 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7rgj is ON HOLD	+	The entry 7rgj is ON HOLD until sometime in the future

	Authors: Lombardo, M.N., Wright, D.L.		Authors: Lombardo, M.N., Wright, D.L.
Line 7:		Line 7:
	Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)		Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Wright, D.L]]
	[[Category: Lombardo, M.N]]		[[Category: Lombardo, M.N]]
		+	[[Category: Wright, D.L]]

OCA: Protected "7rgj" [edit=sysop:move=sysop]

OCA — Wed, 21 Jul 2021 08:04:52 GMT

Protected "7rgj" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:04, 21 July 2021

OCA: New page: '''Unreleased structure''' The entry 7rgj is ON HOLD Authors: Lombardo, M.N., Wright, D.L. Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxo...

OCA — Wed, 21 Jul 2021 08:04:51 GMT

New page: '''Unreleased structure''' The entry 7rgj is ON HOLD Authors: Lombardo, M.N., Wright, D.L. Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxo...

New page

'''Unreleased structure'''

The entry 7rgj is ON HOLD

Authors: Lombardo, M.N., Wright, D.L.

Description: DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)
[[Category: Unreleased Structures]]
[[Category: Wright, D.L]]
[[Category: Lombardo, M.N]]