Structure of PDB 4wdw Chain A Binding Site BS02

Receptor Information
>4wdw Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLY
NNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKK
AQLDYVDLYLIHSPMSLKPGLSPTDENGKVIFDIVDLCTTWEAMEKCKDA
GLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCK
SKDIVLVAYSALGSQRDKRVDPNSPVLLEDPVLCALAKKHKRTPALIALR
YQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYF
Ligand information
Ligand IDWDW
InChIInChI=1S/C15H16N2O/c1-11-5-6-13-12(9-11)10-14(16-13)15(18)17-7-3-2-4-8-17/h2-3,5-6,9-10,16H,4,7-8H2,1H3
InChIKeyQRPYFEVBXZYSAL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc2[nH]c(cc2c1)C(=O)N3CCC=CC3
ACDLabs 12.01O=C(c2cc1cc(ccc1n2)C)N3CC=CCC3
OpenEye OEToolkits 1.9.2Cc1ccc2c(c1)cc([nH]2)C(=O)N3CCC=CC3
FormulaC15 H16 N2 O
Name3,6-dihydropyridin-1(2H)-yl(5-methyl-1H-indol-2-yl)methanone
ChEMBLCHEMBL2413862
DrugBank
ZINCZINC000096282478
PDB chain4wdw Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4wdw Structures of complexes of type 5 17 beta-hydroxysteroid dehydrogenase with structurally diverse inhibitors: insights into the conformational changes upon inhibitor binding.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		Y24 L54 Y55 H117 M120 F306
Binding residue
(residue number reindexed from 1)		Y19 L49 Y50 H112 M115 F298
Annotation score1
Binding affinityBindingDB: IC50=2800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D50 Y55 K84 H117
Catalytic site (residue number reindexed from 1) D45 Y50 K79 H112
Enzyme Commision number 1.1.1.-
1.1.1.188: prostaglandin-F synthase.
1.1.1.210: 3beta-(or 20alpha)-hydroxysteroid dehydrogenase.
1.1.1.239: 3alpha-(17beta)-hydroxysteroid dehydrogenase (NAD(+)).
1.1.1.357: 3alpha-hydroxysteroid 3-dehydrogenase.
1.1.1.53: 3alpha(or 20beta)-hydroxysteroid dehydrogenase.
1.1.1.62: 17beta-estradiol 17-dehydrogenase.
1.1.1.64: testosterone 17beta-dehydrogenase (NADP(+)).
Gene Ontology
Molecular Function
GO:0001758 retinal dehydrogenase activity
GO:0004032 aldose reductase (NADPH) activity
GO:0004033 aldo-keto reductase (NADPH) activity
GO:0004303 estradiol 17-beta-dehydrogenase [NAD(P)+] activity
GO:0004745 all-trans-retinol dehydrogenase (NAD+) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016655 oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
GO:0032052 bile acid binding
GO:0036130 prostaglandin H2 endoperoxidase reductase activity
GO:0036131 prostaglandin D2 11-ketoreductase activity
GO:0045550 geranylgeranyl reductase activity
GO:0045703 ketoreductase activity
GO:0047017 prostaglandin F synthase activity
GO:0047020 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity
GO:0047023 androsterone dehydrogenase activity
GO:0047024 5alpha-androstane-3beta,17beta-diol dehydrogenase activity
GO:0047035 testosterone dehydrogenase (NAD+) activity
GO:0047044 androstan-3-alpha,17-beta-diol dehydrogenase activity
GO:0047045 testosterone 17-beta-dehydrogenase (NADP+) activity
GO:0047086 ketosteroid monooxygenase activity
GO:0047787 Delta4-3-oxosteroid 5beta-reductase activity
GO:0052650 all-trans-retinol dehydrogenase (NADP+) activity
Biological Process
GO:0001523 retinoid metabolic process
GO:0006629 lipid metabolic process
GO:0006693 prostaglandin metabolic process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0007584 response to nutrient
GO:0008202 steroid metabolic process
GO:0008284 positive regulation of cell population proliferation
GO:0008584 male gonad development
GO:0009267 cellular response to starvation
GO:0016488 farnesol catabolic process
GO:0019371 cyclooxygenase pathway
GO:0030216 keratinocyte differentiation
GO:0042448 progesterone metabolic process
GO:0042572 retinol metabolic process
GO:0042574 retinal metabolic process
GO:0043170 macromolecule metabolic process
GO:0044597 daunorubicin metabolic process
GO:0044598 doxorubicin metabolic process
GO:0048385 regulation of retinoic acid receptor signaling pathway
GO:0051897 positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
GO:0061370 testosterone biosynthetic process
GO:0070293 renal absorption
GO:0071277 cellular response to calcium ion
GO:0071379 cellular response to prostaglandin stimulus
GO:0071384 cellular response to corticosteroid stimulus
GO:0071395 cellular response to jasmonic acid stimulus
GO:0071799 cellular response to prostaglandin D stimulus
GO:1900053 negative regulation of retinoic acid biosynthetic process
GO:2000224 regulation of testosterone biosynthetic process
GO:2000353 positive regulation of endothelial cell apoptotic process
GO:2000379 positive regulation of reactive oxygen species metabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4wdw, PDBe:4wdw, PDBj:4wdw
PDBsum4wdw
PubMed25849402
UniProtP42330|AK1C3_HUMAN Aldo-keto reductase family 1 member C3 (Gene Name=AKR1C3)

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