Structure of PDB 2vd1 Chain B

Receptor sequence
>2vd1B (length=198) Species: 9606 (Homo sapiens) [Search protein sequence]
PNYKLTYFNMRGRAEIIRYIFAYLDIQYEDHRIEQADWPEIKSTLPFGKI
PILEVDGLTLHQSLAIARYLTKNTDLAGNTEMEQCHVDAIVDTLDDFMSC
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGNSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
3D structure
PDB2vd1 Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design.
ChainB
Resolution2.25 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 D28 B M11 G13 R14 Q36 M99 W104 Y152 L199 M10 G12 R13 Q35 M98 W103 Y151 L198 MOAD: ic50=0.138uM
PDBbind-CN: -logKd/Ki=6.86,IC50=0.138uM
BindingDB: IC50=94600nM
BS02 GSH B Y8 R14 W39 K43 K50 I51 Q63 S64 Y7 R13 W38 K42 K49 I50 Q62 S63
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:2vd1, PDBe:2vd1, PDBj:2vd1
PDBsum2vd1
PubMed18341273
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

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