Structure of PDB 1pd2 Chain 1 Binding Site BS01

Receptor Information
>1pd2 Chain 1 (length=199) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPNYKLLYFNMRGRAEIIRYIFAYLDIKYEDHRIEQADWPKIKPTLPFGK
IPVLEVEGLTLHQSLAIARYLTKNTDLAGKTELEQCQVDAVVDTLDDFMS
LFPWAEENQDLKERTFNDLLTRQAPHLLKDLDTYLGDKEWFIGNYVTWAD
FYWDICSTTLLVLKPDLLGIYPRLVSLRNKVQAIPAISAWILKRPQTKL
Ligand information
Ligand IDGSH
InChIInChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
InChIKeyRWSXRVCMGQZWBV-WDSKDSINSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NCC(=O)O)C(NC(=O)CCC(C(=O)O)N)CS
OpenEye OEToolkits 1.7.6C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
CACTVS 3.370N[CH](CCC(=O)N[CH](CS)C(=O)NCC(O)=O)C(O)=O
CACTVS 3.370N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N
FormulaC10 H17 N3 O6 S
NameGLUTATHIONE
ChEMBLCHEMBL1543
DrugBankDB00143
ZINCZINC000003830891
PDB chain1pd2 Chain 1 Residue 301 [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]
PDB1pd2 Cloning and crystal structure of hematopoietic prostaglandin D synthase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y8 R14 W39 K43 K50 I51 Q63 S64
Binding residue
(residue number reindexed from 1)		Y8 R14 W39 K43 K50 I51 Q63 S64
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) Y8 R14 W104
Catalytic site (residue number reindexed from 1) Y8 R14 W104
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:0016740 transferase activity
GO:0016853 isomerase activity
GO:0042803 protein homodimerization activity
Biological Process
GO:0001516 prostaglandin biosynthetic process
GO:0006693 prostaglandin metabolic process
GO:0009624 response to nematode
GO:0010269 response to selenium ion
GO:2000255 negative regulation of male germ cell proliferation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1pd2, PDBe:1pd2, PDBj:1pd2
PDBsum1pd2
PubMed9323136
UniProtO35543|HPGDS_RAT Hematopoietic prostaglandin D synthase (Gene Name=Hpgds)

[Back to BioLiP]