Structure of PDB 4edy Chain A Binding Site BS02

Receptor Information
>4edy 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
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand ID9PQ
InChIInChI=1S/C24H26N2O3/c27-17-21-10-5-18-3-1-2-4-22(18)23(21)19-6-8-20(9-7-19)24(28)25-11-12-26-13-15-29-16-14-26/h1-10,27H,11-17H2,(H,25,28)
InChIKeyQFHPEAOPPKNNMS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc2c(c1)ccc(c2c3ccc(cc3)C(=O)NCCN4CCOCC4)CO
ACDLabs 12.01O=C(NCCN1CCOCC1)c4ccc(c3c2ccccc2ccc3CO)cc4
CACTVS 3.370OCc1ccc2ccccc2c1c3ccc(cc3)C(=O)NCCN4CCOCC4
FormulaC24 H26 N2 O3
Name4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
ChEMBLCHEMBL2035655
DrugBank
ZINCZINC000084724429
PDB chain4edy Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4edy Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.
Resolution1.72 Å
Binding residue
(original residue number in PDB)		Y8 F9 M11 G13 R14 Q36 M99 W104 Y152 T159 L199
Binding residue
(residue number reindexed from 1)		Y7 F8 M10 G12 R13 Q35 M98 W103 Y151 T158 L198
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.83,IC50=1480nM
BindingDB: IC50=1480nM
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:4edy, PDBe:4edy, PDBj:4edy
PDBsum4edy
PubMed22546671
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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