Structure of PDB 8cvn Chain A Binding Site BS01

Receptor Information
>8cvn Chain A (length=256) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMVNGKVALVTGAAQGIGRAFAEALLLKGAKVALVDWNLEAGVQCKAALD
EQFEPQKTLFIQCDVADQQQLRDTFRKVVDHFGRLDILVNNAGVNNEKNW
EKTLQINLVSVISGTYLGLDYMSKQNGGEGGIIINMSSLAGLMPVAQQPV
YCASKHGIVGFTRSAALAANLMNSGVRLNAICPGFVNTAILESIEKEENM
GQYIEYKDHIKDMIKYYGILDPPLIANGLITLIEDDALNGAIMKITTSKG
IHFQDY
Ligand information
Ligand IDNAI
InChIInChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBOPGDPNILDQYTO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
FormulaC21 H29 N7 O14 P2
Name1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH
ChEMBLCHEMBL1234616
DrugBankDB00157
ZINCZINC000008215403
PDB chain8cvn Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8cvn Small molecule inhibitors of 15-PGDH exploit a physiologic induced-fit closing system.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Q15 I17 D36 W37 V65 N91 G93 V94 S138 K155 P183 V186 T188
Binding residue
(residue number reindexed from 1)		Q15 I17 D36 W37 V65 N91 G93 V94 S138 K155 P183 V186 T188
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.-
1.1.1.141: 15-hydroxyprostaglandin dehydrogenase (NAD(+)).
1.1.1.232: 15-hydroxyicosatetraenoate dehydrogenase.
Gene Ontology
Molecular Function
GO:0004957 prostaglandin E receptor activity
GO:0016404 15-hydroxyprostaglandin dehydrogenase (NAD+) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0042802 identical protein binding
GO:0051287 NAD binding
GO:0070403 NAD+ binding
Biological Process
GO:0001822 kidney development
GO:0006693 prostaglandin metabolic process
GO:0007179 transforming growth factor beta receptor signaling pathway
GO:0007565 female pregnancy
GO:0007567 parturition
GO:0019372 lipoxygenase pathway
GO:0030728 ovulation
GO:0032355 response to estradiol
GO:0032496 response to lipopolysaccharide
GO:0043065 positive regulation of apoptotic process
GO:0045471 response to ethanol
GO:0045786 negative regulation of cell cycle
GO:0070493 thrombin-activated receptor signaling pathway
GO:0097070 ductus arteriosus closure
GO:1904707 positive regulation of vascular associated smooth muscle cell proliferation
GO:1905828 regulation of prostaglandin catabolic process
Cellular Component
GO:0005615 extracellular space
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016323 basolateral plasma membrane
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8cvn, PDBe:8cvn, PDBj:8cvn
PDBsum8cvn
PubMed36774348
UniProtP15428|PGDH_HUMAN 15-hydroxyprostaglandin dehydrogenase [NAD(+)] (Gene Name=HPGD)

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