Structure of PDB 5yx1 Chain B Binding Site BS02

Receptor Information
>5yx1 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 IDUX4
InChIInChI=1S/C21H29N5O4S/c1-4-30-21(29)25-11-9-24(10-12-25)20(28)23-17-14(3)16-18(31-17)22-15-6-5-13(2)7-8-26(15)19(16)27/h13H,4-12H2,1-3H3,(H,23,28)/t13-/m1/s1
InChIKeyXBHQVTSPEFNYKC-CYBMUJFWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(OCC)N1CCN(CC1)C(=O)Nc2sc3c(c2C)C(N4C(=N3)CCC(C)CC4)=O
OpenEye OEToolkits 2.0.6CCOC(=O)N1CCN(CC1)C(=O)Nc2c(c3c(s2)N=C4CC[C@H](CCN4C3=O)C)C
CACTVS 3.385CCOC(=O)N1CCN(CC1)C(=O)Nc2sc3N=C4CC[C@@H](C)CCN4C(=O)c3c2C
OpenEye OEToolkits 2.0.6CCOC(=O)N1CCN(CC1)C(=O)Nc2c(c3c(s2)N=C4CCC(CCN4C3=O)C)C
CACTVS 3.385CCOC(=O)N1CCN(CC1)C(=O)Nc2sc3N=C4CC[CH](C)CCN4C(=O)c3c2C
FormulaC21 H29 N5 O4 S
Nameethyl 4-[(8R)-3,8-dimethyl-4-oxo-4,6,7,8,9,10-hexahydrothieno[2',3':4,5]pyrimido[1,2-a]azepin-2-yl]carbamoylpiperazine-1-carboxylate
ChEMBL
DrugBank
ZINCZINC000004111000
PDB chain5yx1 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yx1 Crystal structure of hematopoietic prostaglandin D synthase in complex with U004
Resolution1.39 Å
Binding residue
(original residue number in PDB)		M11 G13 W39 W104 A105 Y152 T159
Binding residue
(residue number reindexed from 1)		M10 G12 W38 W103 A104 Y151 T158
Annotation score1
Enzymatic activity
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:5yx1, PDBe:5yx1, PDBj:5yx1
PDBsum5yx1
PubMed
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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