Structure of PDB 4ec0 Chain A Binding Site BS02

Receptor Information
>4ec0 Chain A (length=199) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGK
IPILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMS
CFPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWAD
FYWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand ID7PQ
InChIInChI=1S/C24H27N3O2/c25-17-21-10-5-18-3-1-2-4-22(18)23(21)19-6-8-20(9-7-19)24(28)26-11-12-27-13-15-29-16-14-27/h1-10H,11-17,25H2,(H,26,28)
InChIKeyLJXMOYXCVXIDDM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCCN1CCOCC1)c4ccc(c3c2ccccc2ccc3CN)cc4
OpenEye OEToolkits 1.7.6c1ccc2c(c1)ccc(c2c3ccc(cc3)C(=O)NCCN4CCOCC4)CN
CACTVS 3.370NCc1ccc2ccccc2c1c3ccc(cc3)C(=O)NCCN4CCOCC4
FormulaC24 H27 N3 O2
Name4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
ChEMBLCHEMBL2035656
DrugBank
ZINCZINC000084724434
PDB chain4ec0 Chain A Residue 203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4ec0 Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		Y8 M11 G13 R14 M99 W104 Y152 T159 L199
Binding residue
(residue number reindexed from 1)		Y8 M11 G13 R14 M99 W104 Y152 T159 L199
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.07,IC50=845nM
BindingDB: IC50=845nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ec0, PDBe:4ec0, PDBj:4ec0
PDBsum4ec0
PubMed22546671
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

[Back to BioLiP]