Structure of PDB 2vd0 Chain B Binding Site BS01
Receptor Information
>2vd0 Chain B (length=198) Species:
9606
(Homo sapiens) [
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PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKI
PILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSC
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand ID
D27
InChI
InChI=1S/C18H17NO5/c1-23-15-9-7-12(11-16(15)24-2)8-10-17(20)19-14-6-4-3-5-13(14)18(21)22/h3-11H,1-2H3,(H,19,20)(H,21,22)/b10-8+
InChIKey
NZHGWWWHIYHZNX-CSKARUKUSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
COc1ccc(cc1OC)\C=C\C(=O)Nc2ccccc2C(=O)O
CACTVS 3.341
COc1ccc(/C=C/C(=O)Nc2ccccc2C(O)=O)cc1OC
CACTVS 3.341
COc1ccc(C=CC(=O)Nc2ccccc2C(O)=O)cc1OC
ACDLabs 10.04
O=C(O)c1ccccc1NC(=O)\C=C\c2cc(OC)c(OC)cc2
OpenEye OEToolkits 1.5.0
COc1ccc(cc1OC)C=CC(=O)Nc2ccccc2C(=O)O
Formula
C18 H17 N O5
Name
2-{[(2E)-3-(3,4-dimethoxyphenyl)prop-2-enoyl]amino}benzoic acid
ChEMBL
CHEMBL415324
DrugBank
DB07615
ZINC
ZINC000000000797
PDB chain
2vd0 Chain B Residue 1200 [
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Receptor-Ligand Complex Structure
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PDB
2vd0
Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design.
Resolution
2.2 Å
Binding residue
(original residue number in PDB)
M11 G13 R14 M99 W104 A105 Y152 L199
Binding residue
(residue number reindexed from 1)
M10 G12 R13 M98 W103 A104 Y151 L198
Annotation score
1
Binding affinity
MOAD
: ic50=11.6uM
PDBbind-CN
: -logKd/Ki=4.94,IC50=11.6uM
BindingDB: IC50=11600nM
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:2vd0
,
PDBe:2vd0
,
PDBj:2vd0
PDBsum
2vd0
PubMed
18341273
UniProt
O60760
|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)
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