Structure of PDB 3vi5 Chain D Binding Site BS01

Receptor Information
>3vi5 Chain D (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
FPWAEKKQDVKEQMFNELLTYNAPHLMQDLDTYLGGREWLIGMSVTWADF
YWEICSTTLLVFKPDLLDNHPRLVTLRKKVQAIPAVANWIKRRPQTKL
Ligand information
Ligand IDM4M
InChIInChI=1S/C20H15N3O7S2/c21-18-15(32(28,29)30)9-14(23-10-5-7-11(8-6-10)31(22,26)27)16-17(18)20(25)13-4-2-1-3-12(13)19(16)24/h1-9,23H,21H2,(H2,22,26,27)(H,28,29,30)
InChIKeyRRARWTAYDLOASH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2c1ccc2c(c1)C(=O)c3c(cc(c(c3C2=O)N)S(=O)(=O)O)Nc4ccc(cc4)S(=O)(=O)N
ACDLabs 12.01O=S(=O)(N)c1ccc(cc1)Nc4c3C(=O)c2ccccc2C(=O)c3c(c(c4)S(=O)(=O)O)N
CACTVS 3.370Nc1c2C(=O)c3ccccc3C(=O)c2c(Nc4ccc(cc4)[S](N)(=O)=O)cc1[S](O)(=O)=O
FormulaC20 H15 N3 O7 S2
Name1-amino-9,10-dioxo-4-[(4-sulfamoylphenyl)amino]-9,10-dihydroanthracene-2-sulfonic acid;
1-amino-4-(4-aminosulfonyl)phenylamino-anthraquinone-2-sulfonic acid
ChEMBLCHEMBL2163818
DrugBank
ZINCZINC000020530820
PDB chain3vi5 Chain D Residue 804 [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]
PDB3vi5 Human hematopoietic prostaglandin D synthase inhibitor complex structures
Resolution2.0 Å
Binding residue
(original residue number in PDB)
G613 R614 K650 M699 W704
Binding residue
(residue number reindexed from 1)
G12 R13 K49 M98 W103
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.68,IC50=2.1uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y608 R614 R619 W704
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:3vi5, PDBe:3vi5, PDBj:3vi5
PDBsum3vi5
PubMed22418579
UniProtO60760|HPGDS_HUMAN Hematopoietic prostaglandin D synthase (Gene Name=HPGDS)

[Back to BioLiP]