Structure of PDB 4dbw Chain A Binding Site BS02

Receptor Information
>4dbw Chain A (length=315) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLY
NNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKK
AQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCK
DAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDF
CKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALI
ALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHY
FNSDSFASHPNYPYS
Ligand information
Ligand ID511
InChIInChI=1S/C18H14ClNO4/c1-24-14-6-7-16-15(9-14)12(8-17(21)22)10-20(16)18(23)11-2-4-13(19)5-3-11/h2-7,9-10H,8H2,1H3,(H,21,22)
InChIKeyDHEMTWWLRLOBKI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370COc1ccc2n(cc(CC(O)=O)c2c1)C(=O)c3ccc(Cl)cc3
OpenEye OEToolkits 1.7.6COc1ccc2c(c1)c(cn2C(=O)c3ccc(cc3)Cl)CC(=O)O
ACDLabs 12.01Clc1ccc(cc1)C(=O)n3c2ccc(OC)cc2c(c3)CC(=O)O
FormulaC18 H14 Cl N O4
Name[1-(4-chlorobenzoyl)-5-methoxy-1H-indol-3-yl]acetic acid;
2'-desmethyl-indomethacin
ChEMBLCHEMBL503179
DrugBank
ZINCZINC000004298622
PDB chain4dbw 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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PDB4dbw Development of potent and selective indomethacin analogues for the inhibition of AKR1C3 (Type 5 17 beta-hydroxysteroid dehydrogenase/prostaglandin F synthase) in castrate-resistant prostate cancer.
Resolution1.802 Å
Binding residue
(original residue number in PDB)		Y24 L54 Y55 H117 S118 M120 N167 W227 F306 Y319
Binding residue
(residue number reindexed from 1)		Y19 L49 Y50 H112 S113 M115 N162 W222 F301 Y314
Annotation score1
Binding affinityMOAD: ic50=0.1uM
BindingDB: IC50=0.96nM
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:4dbw, PDBe:4dbw, PDBj:4dbw
PDBsum4dbw
PubMed23432095
UniProtP42330|AK1C3_HUMAN Aldo-keto reductase family 1 member C3 (Gene Name=AKR1C3)

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