5liy - Revision history

OCA at 18:28, 18 October 2023

2023-10-18T18:28:39Z

←Older revision		Revision as of 18:28, 18 October 2023
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	<StructureSection load='5liy' size='340' side='right'caption='[[5liy]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5liy' size='340' side='right'caption='[[5liy]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5liy]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LIY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5liy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LIY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DQP:{5-CHLORO-2-[(PENTABROMOBENZYL)CARBAMOYL]PHENOXY}ACETIC+ACID'>DQP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, ~~<scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 2.05Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DQP:{5-CHLORO-2-[(PENTABROMOBENZYL)CARBAMOYL]PHENOXY}ACETIC+ACID'>DQP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AKR1B10, AKR1B11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=5liy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5liy OCA], [https://pdbe.org/5liy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5liy RCSB], [https://www.ebi.ac.uk/pdbsum/5liy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5liy 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=5liy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5liy OCA], [~~http~~://pdbe.org/5liy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5liy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5liy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5liy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AK1BA_HUMAN AK1BA_HUMAN]] Acts as all-trans-retinaldehyde reductase. Can efficiently reduce aliphatic and aromatic aldehydes, and is less active on hexoses (in vitro). May be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs.<ref>PMID:18087047</ref>	+	[https://www.uniprot.org/uniprot/AK1BA_HUMAN AK1BA_HUMAN] Acts as all-trans-retinaldehyde reductase. Can efficiently reduce aliphatic and aromatic aldehydes, and is less active on hexoses (in vitro). May be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs.<ref>PMID:18087047</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cousido-Siah, A]]	+	[[Category: Cousido-Siah A]]
-	[[Category: Fanfrlik, J]]	+	[[Category: Fanfrlik J]]
-	[[Category: Hobza, P]]	+	[[Category: Hobza P]]
-	[[Category: Kamlar, M]]	+	[[Category: Kamlar M]]
-	[[Category: Mitschler, A]]	+	[[Category: Mitschler A]]
-	[[Category: Podjarny, A]]	+	[[Category: Podjarny A]]
-	[[Category: Ruiz~~, F X~~]]	+	[[Category: Ruiz FX]]
-	[[Category: Vesely, J]]	+	[[Category: Vesely J]]
-	~~[[Category: Aldo-keto reductase]]~~	+
-	~~[[Category: Alpha-beta tim barrel]]~~	+
-	~~[[Category: Cytosol]]~~	+
-	~~[[Category: Halogenated ligand]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:38, 12 August 2020

2020-08-12T10:38:59Z

←Older revision		Revision as of 10:38, 12 August 2020
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	==Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204==		==Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204==
-	<StructureSection load='5liy' size='340' side='right' caption='[[5liy]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5liy' size='340' side='right'caption='[[5liy]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5liy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LIY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5liy]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LIY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQP:{5-CHLORO-2-[(PENTABROMOBENZYL)CARBAMOYL]PHENOXY}ACETIC+ACID'>DQP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DQP:{5-CHLORO-2-[(PENTABROMOBENZYL)CARBAMOYL]PHENOXY}ACETIC+ACID'>DQP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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=5liy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5liy OCA], [http://pdbe.org/5liy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5liy RCSB], [http://www.ebi.ac.uk/pdbsum/5liy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5liy ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AKR1B10, AKR1B11 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5liy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5liy OCA], [http://pdbe.org/5liy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5liy RCSB], [http://www.ebi.ac.uk/pdbsum/5liy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5liy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5liy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5liy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldo-keto reductase 3D structures\|Aldo-keto reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Cousido-Siah, A]]		[[Category: Cousido-Siah, A]]
	[[Category: Fanfrlik, J]]		[[Category: Fanfrlik, J]]

OCA at 17:45, 19 October 2016

2016-10-19T17:45:15Z

←Older revision		Revision as of 17:45, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5liy is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204==
		+	<StructureSection load='5liy' size='340' side='right' caption='[[5liy]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5liy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LIY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LIY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DQP:{5-CHLORO-2-[(PENTABROMOBENZYL)CARBAMOYL]PHENOXY}ACETIC+ACID'>DQP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</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=5liy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5liy OCA], [http://pdbe.org/5liy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5liy RCSB], [http://www.ebi.ac.uk/pdbsum/5liy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5liy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AK1BA_HUMAN AK1BA_HUMAN]] Acts as all-trans-retinaldehyde reductase. Can efficiently reduce aliphatic and aromatic aldehydes, and is less active on hexoses (in vitro). May be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs.<ref>PMID:18087047</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhibitor IDD388, we have synthesized a series of derivatives bearing the same halophenoxyacetic acid moiety with increasing number of bromine (Br) atoms on its aryl moiety. Next, by means of IC50 measurements, X-ray crystallography, WaterMap analysis and advanced binding free energy calculations with a quantum-mechanical (QM) approach, we have studied their Structure-Activity Relationship (SAR) against both enzymes. The introduction of Br substituents decreases AR inhibition potency but improves it in the case of AKR1B10. Indeed, the Br atoms in ortho position may impede these drugs to fit into the AR prototypical specificity pocket. For AKR1B10, the smaller aryl moieties of MK181 and IDD388 can bind into the external loop A subpocket. Instead, the bulkier MK184, MK319 and MK204 open an inner specificity pocket in AKR1B10 characterized by a pi-pi stacking interaction of their aryl moieties and Trp112 side chain in the native conformation (not possible in AR). Among the three compounds, only MK204 can make a strong halogen bond with the protein (-4.4 kcal/mol, using QM calculations), while presenting the lowest desolvation cost among all the series, translated into the most selective and inhibitory potency AKR1B10 (IC50 = 80 nM). Overall, SAR of these IDD388 polyhalogenated derivatives have unveiled several distinctive AKR1B10 features (shape, flexibility, hydration), that can be exploited to design novel types of AKR1B10 selective drugs.

-	~~Authors:~~ Cousido-Siah, A., Ruiz, ~~F.X.~~, Mitschler, A., ~~Fanfrlik~~, J., ~~Kamlar~~, ~~M., Vesely~~, J., Hobza, P., Podjarny~~, A~~.	+	IDD388 polyhalogenated derivatives as probes for an improved structure-based selectivity of AKR1B10 inhibitors.,Cousido-Siah A, Ruiz FX, Fanfrlik J, Gimenez-Dejoz J, Mitschler A, Kamlar M, Vesely J, Ajani H, Pares X, Farres J, Hobza P, Podjarny AD ACS Chem Biol. 2016 Jun 30. PMID:27359042<ref>PMID:27359042</ref>

-	~~Description: Crystal structure~~ of ~~human AKR1B10 complexed with NADP+ and~~ the ~~inhibitor MK204~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Podjarny, A]]~~	+	<div class="pdbe-citations 5liy" style="background-color:#fffaf0;"></div>
-	~~[[Category: Hobza, P]]~~	+	== References ==
-	~~[[Category: Mitschler, A]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Cousido-Siah, A]]		[[Category: Cousido-Siah, A]]
-	[[Category: Kamlar, M]]
-	[[Category: Ruiz, F.X]]
	[[Category: Fanfrlik, J]]		[[Category: Fanfrlik, J]]
		+	[[Category: Hobza, P]]
		+	[[Category: Kamlar, M]]
		+	[[Category: Mitschler, A]]
		+	[[Category: Podjarny, A]]
		+	[[Category: Ruiz, F X]]
	[[Category: Vesely, J]]		[[Category: Vesely, J]]
		+	[[Category: Aldo-keto reductase]]
		+	[[Category: Alpha-beta tim barrel]]
		+	[[Category: Cytosol]]
		+	[[Category: Halogenated ligand]]
		+	[[Category: Oxidoreductase]]

OCA at 14:32, 10 August 2016

2016-08-10T14:32:07Z

←Older revision		Revision as of 14:32, 10 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Cousido-Siah, A., Ruiz, F.X., Mitschler, A., Fanfrlik, J., Kamlar, M., Vesely, J., Hobza, P., Podjarny, A.		Authors: Cousido-Siah, A., Ruiz, F.X., Mitschler, A., Fanfrlik, J., Kamlar, M., Vesely, J., Hobza, P., Podjarny, A.

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

2016-07-27T14:00:04Z

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

←Older revision

Revision as of 14:00, 27 July 2016

OCA: New page: '''Unreleased structure''' The entry 5liy is ON HOLD Authors: Cousido-Siah, A., Ruiz, F.X., Mitschler, A., Fanfrlik, J., Kamlar, M., Vesely, J., Hobza, P., Podjarny, A. Description: Cr...

2016-07-27T14:00:03Z

New page: '''Unreleased structure''' The entry 5liy is ON HOLD Authors: Cousido-Siah, A., Ruiz, F.X., Mitschler, A., Fanfrlik, J., Kamlar, M., Vesely, J., Hobza, P., Podjarny, A. Description: Cr...

New page

'''Unreleased structure'''

The entry 5liy is ON HOLD

Authors: Cousido-Siah, A., Ruiz, F.X., Mitschler, A., Fanfrlik, J., Kamlar, M., Vesely, J., Hobza, P., Podjarny, A.

Description: Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK204
[[Category: Unreleased Structures]]
[[Category: Podjarny, A]]
[[Category: Hobza, P]]
[[Category: Mitschler, A]]
[[Category: Cousido-Siah, A]]
[[Category: Kamlar, M]]
[[Category: Ruiz, F.X]]
[[Category: Fanfrlik, J]]
[[Category: Vesely, J]]