Structure of PDB 3ee2 Chain A Binding Site BS02

Receptor Information
>3ee2 Chain A (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
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAIANWIKRRPQTKL
Ligand information
Ligand IDNZO
InChIInChI=1S/C14H11N3O3S/c1-20-14(19)17-13-15-9-5-4-8(7-10(9)16-13)12(18)11-3-2-6-21-11/h2-7H,1H3,(H2,15,16,17,19)
InChIKeyKYRVNWMVYQXFEU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(c2cc1c(nc(NC(=O)OC)n1)cc2)c3sccc3
OpenEye OEToolkits 1.5.0COC(=O)Nc1[nH]c2cc(ccc2n1)C(=O)c3cccs3
CACTVS 3.341COC(=O)Nc1[nH]c2cc(ccc2n1)C(=O)c3sccc3
FormulaC14 H11 N3 O3 S
Namenocodazole;
methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate
ChEMBLCHEMBL9514
DrugBankDB08313
ZINCZINC000000056509
PDB chain3ee2 Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ee2 Identification and characterisation of new inhibitors for the human hematopoietic prostaglandin D(2) synthase
Resolution1.91 Å
Binding residue
(original residue number in PDB)		R14 M99 W104 Y152
Binding residue
(residue number reindexed from 1)		R13 M98 W103 Y151
Annotation score1
Binding affinityMOAD: ic50~65uM
PDBbind-CN: -logKd/Ki=4.19,IC50=65uM
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:3ee2, PDBe:3ee2, PDBj:3ee2
PDBsum3ee2
PubMed19939518
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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