PDBsum entry 1v40

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
Protein chain
198 a.a. *
GSH ×4
O16 ×4
GOL ×6
_MG ×2
Waters ×1462
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: First inhibitor complex structure of human hematopoietic pro d synthase
Structure: Glutathione-requiring prostaglandin d synthase. Chain: a, b, c, d. Synonym: glutathione-dependent pgd synthetase, prostaglandi isomerase, hematopoietic prostaglandin d synthase, h-pgds. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
1.90Å     R-factor:   0.195     R-free:   0.215
Authors: T.Inoue,Y.Okano,Y.Kado,K.Aritake,D.Irikura,N.Uodome,S.Kinuga N.Okazaki,H.Matsumura,Y.Kai,Y.Urade
Key ref: T.Inoue et al. (2004). First determination of the inhibitor complex structure of human hematopoietic prostaglandin D synthase. J Biochem, 135, 279-283. PubMed id: 15113825
07-Nov-03     Release date:   07-Nov-04    
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Protein chains
Pfam   ArchSchema ?
O60760  (HPGDS_HUMAN) -  Hematopoietic prostaglandin D synthase
199 a.a.
198 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: E.C.  - Glutathione transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: RX + glutathione = HX + R-S-glutathione
Bound ligand (Het Group name = GSH)
corresponds exactly
= HX
+ R-S-glutathione
   Enzyme class 3: E.C.  - Prostaglandin-D synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (5Z,13E,15S)-9-alpha,11-alpha-epidioxy-15-hydroxyprosta-5,13-dienoate = (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
= (5Z,13E,15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate
      Cofactor: Glutathione
Bound ligand (Het Group name = GSH) corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     small molecule metabolic process   12 terms 
  Biochemical function     transferase activity     8 terms  


J Biochem 135:279-283 (2004)
PubMed id: 15113825  
First determination of the inhibitor complex structure of human hematopoietic prostaglandin D synthase.
T.Inoue, Y.Okano, Y.Kado, K.Aritake, D.Irikura, N.Uodome, N.Okazaki, S.Kinugasa, H.Shishitani, H.Matsumura, Y.Kai, Y.Urade.
Hematopoietic prostaglandin (PG) D synthase (H-PGDS) is responsible for the production of PGD(2) as an allergy or inflammation mediator in mast and Th2 cells. We determined the X-ray structure of human H-PGDS complexed with an inhibitor, 2-(2'-benzothiazolyl)-5-styryl-3-(4'-phthalhydrazidyl) tetrazolium chloride (BSPT) at 1.9 A resolution in the presence of Mg(2+). The styryl group of the inhibitor penetrated to the bottom of the active site cleft, and the tetrazole ring was stabilized by the stacking interaction with Trp104, inducing large movement around the alpha5-helix, which caused the space group of the complex crystal to change from P2(1) to P1 upon binding of BSPT. The phthalhydrazidyl group of BSPT exhibited steric hindrance due to the cofactor, glutathione (GSH), increasing the IC(50) value of BSPT for human H-PGDS from 36.2 micro M to 98.1 micro M upon binding of Mg(2+), because the K(m) value of GSH for human H-PGDS was decreased from 0.60 micro M in the presence of EDTA to 0.14 micro M in the presence of Mg(2+). We have to avoid steric hindrance of the GSH molecule that was stabilized by intracellular Mg(2+) in the mM range in the cytosol for further development of structure-based anti-allergic drugs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20122226 P.Paragi-Vedanthi, and M.Doble (2010).
Comparison of PGH2 binding site in prostaglandin synthases.
  BMC Bioinformatics, 11, S51.  
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