2VCZ

Complex structure of prostaglandin D2 synthase at 1.95A.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design.

Hohwy, M.Spadola, L.Lundquist, B.Hawtin, P.Dahmen, J.Groth-Clausen, I.Nilsson, E.Persdotter, S.Von Wachenfeldt, K.Folmer, R.H.A.Edman, K.

(2008) J.Med.Chem. 51: 2178

  • DOI: 10.1021/jm701509k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the discovery of novel inhibitors of prostaglandin D2 synthase (PGDS) through fragment-based lead generation and structure-based drug design. A library of 2500 low-molecular-weight compounds was screened using 2D nuclear magnetic resonanc ...

    We describe the discovery of novel inhibitors of prostaglandin D2 synthase (PGDS) through fragment-based lead generation and structure-based drug design. A library of 2500 low-molecular-weight compounds was screened using 2D nuclear magnetic resonance (NMR), leading to the identification of 24 primary hits. Structure determination of protein-ligand complexes with the hits enabled a hit optimization process, whereby we harvested increasingly more potent inhibitors out of our corporate compound collection. Two iterative cycles were carried out, comprising NMR screening, molecular modeling, X-ray crystallography, and in vitro biochemical testing. Six novel high-resolution PGDS complex structures were determined, and 300 hit analogues were tested. This rational drug design procedure culminated in the discovery of 24 compounds with an IC 50 below 1 microM in the in vitro assay. The best inhibitor (IC 50 = 21 nM) is one of the most potent inhibitors of PGDS to date. As such, it may enable new functional in vivo studies of PGDS and the prostaglandin metabolism pathway.


    Organizational Affiliation

    Global Structural Chemistry and Global Compound Sciences, AstraZeneca Research and Development, S-43183 Mölndal, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE-REQUIRING PROSTAGLANDIN D SYNTHASE
A, B, C, D
199Homo sapiensMutation(s): 0 
Gene Names: HPGDS (GSTS, PGDS, PTGDS2)
EC: 5.3.99.2
Find proteins for O60760 (Homo sapiens)
Go to Gene View: HPGDS
Go to UniProtKB:  O60760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VC3
Query on VC3

Download SDF File 
Download CCD File 
B
3-(4-nitrophenyl)-1H-pyrazole
C9 H7 N3 O2
IPIYADCDDIUVPS-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
A, B, C, D
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • Space Group: I 41
Unit Cell:
Length (Å)Angle (°)
a = 123.429α = 90.00
b = 123.429β = 90.00
c = 106.273γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance