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==Complex of Aldose Reductase with NADP+ and simaltaneously bound competetive inhibitors Fidarestat and IDD594. Concentration of Fidarestat in soaking solution is less than concentration of IDD594.== | |||
<StructureSection load='2pfh' size='340' side='right'caption='[[2pfh]], [[Resolution|resolution]] 0.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2pfh]] 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=2PFH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PFH FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.85Å</td></tr> | |||
| | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FID:(2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4-IMIDAZOLIDINE]-2,5-DIONE'>FID</scene>, <scene name='pdbligand=LDT:IDD594'>LDT</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=2pfh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pfh OCA], [https://pdbe.org/2pfh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pfh RCSB], [https://www.ebi.ac.uk/pdbsum/2pfh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pfh ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ALDR_HUMAN ALDR_HUMAN] Catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols with a broad range of catalytic efficiencies. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pf/2pfh_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pfh ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) =6.5nM) and IDD594 (594; K(d) =61nM), which bind to h-Aldose Reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differs 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken in consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used. SYNOPSIS: Crystals soaked simultaneously with two inhibitors and corresponding models of the complex of Aldose Reductase with two inhibitors solved at subatomic resolution reveal differences between binding of inhibitors with enzyme in solution and in crystals, which has to be taken into account in FBS-X screenings Proteins 2012. (c) 2012 Wiley Periodicals, Inc. | |||
Crystal packing modifies ligand binding affinity: The case of aldose reductase.,Cousido-Siah A, Petrova T, Hazemann I, Mitschler A, Ruiz FX, Howard E, Ginell S, Atmanene C, Van Dorsselaer A, Sanglier-Cianferani S, Joachimiak A, Podjarny A Proteins. 2012 Jul 2. doi: 10.1002/prot.24136. PMID:22752989<ref>PMID:22752989</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2pfh" style="background-color:#fffaf0;"></div> | |||
== | ==See Also== | ||
*[[Aldose reductase 3D structures|Aldose reductase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Cousido | [[Category: Cousido A]] | ||
[[Category: Ginell | [[Category: Ginell S]] | ||
[[Category: Hazemann | [[Category: Hazemann I]] | ||
[[Category: Joachimiak | [[Category: Joachimiak A]] | ||
[[Category: Mitschler | [[Category: Mitschler A]] | ||
[[Category: Petrova | [[Category: Petrova T]] | ||
[[Category: Podjarny | [[Category: Podjarny A]] | ||