9s04
From Proteopedia
(Difference between revisions)
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| - | '''Unreleased structure''' | ||
| - | + | ==PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone== | |
| + | <StructureSection load='9s04' size='340' side='right'caption='[[9s04]], [[Resolution|resolution]] 1.57Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9s04]] is a 5 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=9S04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9S04 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]] 1.57Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1JKQ:1-[2,4-bis(fluoranyl)phenyl]-2-(1,2,4-triazol-1-yl)ethanone'>A1JKQ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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=9s04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9s04 OCA], [https://pdbe.org/9s04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9s04 RCSB], [https://www.ebi.ac.uk/pdbsum/9s04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9s04 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Disease == | ||
| + | [https://www.uniprot.org/uniprot/P5CR1_HUMAN P5CR1_HUMAN] Defects in PYCR1 are the cause of cutis laxa autosomal recessive type 2B (ARCL2B) [MIM:[https://omim.org/entry/612940 612940]. A multisystem disorder characterized by the appearance of premature aging, wrinkled and lax skin with reduced elasticity, joint laxity, craniofacial dysmorphic features, intrauterine growth retardation with some degree of postnatal growth deficiency, and developmental delay.<ref>PMID:19648921</ref> <ref>PMID:19576563</ref> Defects in PYCR1 are the cause of cutis laxa, autosomal recessive, type 3B (ARCL3B) [MIM:[https://omim.org/entry/614438 614438]. ARCL3B is a disorder characterized by an aged appearance with distinctive facial features, sparse hair, ophthalmologic abnormalities, intrauterine growth retardation, and cutis laxa.<ref>PMID:19648921</ref> <ref>PMID:22052856</ref> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/P5CR1_HUMAN P5CR1_HUMAN] Housekeeping enzyme that catalyzes the last step in proline biosynthesis. Can utilize both NAD and NADP, but has higher affinity for NAD. Involved in the cellular response to oxidative stress.<ref>PMID:19648921</ref> <ref>PMID:16730026</ref> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pyrroline-5-carboxylate (P5C) reductase catalyzes the final step in proline biosynthesis. Human P5C reductase isoform 1 (PYCR1) has emerged as a key metabolic enzyme supporting cancer progression through its roles in redox homeostasis, collagen production, and the proline-P5C cycle. Despite its relevance as a therapeutic target, structural and chemical efforts to inhibit PYCR1 remain limited and have largely focused on proline analogs. Here, we report the first crystallographic fragment screening (XFS) campaign against PYCR1, employing a chemically diverse library of 96 compounds. We solved twelve co-crystal structures, featuring ligands occupying the P5C and NADH binding pockets, including dual-site ligands that span both regions. Among the newly identified moieties, sulfonamide and sulfamate groups emerged as notable isosteric replacements for the carboxylate group in the PYCR1 active site. Aromatic substituents in several compounds revealed a cryptic subpocket near the nicotinamide-binding site. Interestingly, halogen-substituted aromatic rings, often present in known PYCR1 inhibitors, exhibited distinct binding orientations, reflecting the flexibility and diversity of interactions in the binding subpockets. High-resolution structures revealed ligand-induced conformational changes in PYCR1, some involving significant rearrangements. Molecular dynamics simulations indicated that these conformations are accessible in the ligand-free enzyme, underscoring the intrinsic plasticity of PYCR1's active site. | ||
| - | + | Crystallographic fragment screening reveals new starting points for PYCR1 inhibitor design.,Ragin-Oh W, Czerwonka D, Tran LH, Forlani G, Ruszkowski M Bioorg Chem. 2025 Sep 23;165:109024. doi: 10.1016/j.bioorg.2025.109024. PMID:41016381<ref>PMID:41016381</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 9s04" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Homo sapiens]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Czerwonka D]] | ||
| + | [[Category: Ragin-Oh W]] | ||
| + | [[Category: Ruszkowski M]] | ||
Current revision
PYCR1 in complex with 1-(2,4-Difluorophenyl)-2-(1H-1,2,4-triazol-1- yl)ethanone
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