Structure of PDB 3kxo Chain B Binding Site BS02

Receptor Information
>3kxo Chain B (length=198) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKI
PILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSC
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand IDKXO
InChIInChI=1S/C19H19F4N3O/c20-15-3-1-2-13(10-15)17-5-4-14(11-24-17)18(27)25-16-6-8-26(9-7-16)12-19(21,22)23/h1-5,10-11,16H,6-9,12H2,(H,25,27)
InChIKeyLPUCBGGXXIUBAZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)F)c2ccc(cn2)C(=O)NC3CCN(CC3)CC(F)(F)F
CACTVS 3.352Fc1cccc(c1)c2ccc(cn2)C(=O)NC3CCN(CC3)CC(F)(F)F
FormulaC19 H19 F4 N3 O
Name6-(3-fluorophenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
ChEMBLCHEMBL1233897
DrugBank
ZINCZINC000058649826
PDB chain3kxo Chain B Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kxo Discovery of an oral potent selective inhibitor of hematopoietic prostaglandin D synthase
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F9 M11 R14 Q36 M99 W104
Binding residue
(residue number reindexed from 1)		F8 M10 R13 Q35 M98 W103
Annotation score1
Binding affinityBindingDB: IC50=200nM,Kd=20nM,EC50=35nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y8 R14 R19 W104
Catalytic site (residue number reindexed from 1) Y7 R13 R18 W103
Enzyme Commision number 2.5.1.18: glutathione transferase.
5.3.99.2: prostaglandin-D synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004364 glutathione transferase activity
GO:0004667 prostaglandin-D synthase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0016740 transferase activity
GO:0016853 isomerase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0001516 prostaglandin biosynthetic process
GO:0006693 prostaglandin metabolic process
GO:0007165 signal transduction
GO:0007626 locomotory behavior
GO:0009624 response to nematode
GO:0010269 response to selenium ion
GO:2000255 negative regulation of male germ cell proliferation
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kxo, PDBe:3kxo, PDBj:3kxo
PDBsum3kxo
PubMed
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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