Structure of PDB 5aiv Chain D Binding Site BS01

Receptor Information
>5aiv Chain D (length=198) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKI
PILEVDGLTLHQSLAIARYLTENTDLAGNTEMEQCHVDAIVDTLDDFMSC
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand IDM1W
InChIInChI=1S/C15H16N4O3/c1-21-9-3-7-17-14(20)15-18-13(19-22-15)11-4-2-5-12-10(11)6-8-16-12/h2,4-6,8,16H,3,7,9H2,1H3,(H,17,20)
InChIKeyBPSPJIVDNLKGAJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6COCCCNC(=O)c1nc(no1)c2cccc3c2cc[nH]3
CACTVS 3.385COCCCNC(=O)c1onc(n1)c2cccc3[nH]ccc23
ACDLabs 12.01O=C(c1nc(no1)c3c2ccnc2ccc3)NCCCOC
FormulaC15 H16 N4 O3
Name3-(1H-indol-4-yl)-N-(3-methoxypropyl)-1,2,4-oxadiazole-5-carboxamide
ChEMBLCHEMBL3425952
DrugBank
ZINCZINC000012391841
PDB chain5aiv Chain D Residue 1200 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5aiv Identification of Indole Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase (Hh-Pgds).
Resolution2.04 Å
Binding residue
(original residue number in PDB)		M11 G13 R14 Q36 M99 W104
Binding residue
(residue number reindexed from 1)		M10 G12 R13 Q35 M98 W103
Annotation score1
Binding affinityMOAD: Kd=0.65uM
BindingDB: IC50=170nM,Kd=650nM
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:5aiv, PDBe:5aiv, PDBj:5aiv
PDBsum5aiv
PubMed25978964
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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