3EE2

Structure of human prostaglandin D-synthase (hGSTS1-1) in complex with nocodazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Identification and characterisation of new inhibitors for the human hematopoietic prostaglandin D(2) synthase

Weber, J.E.Oakley, A.J.Christ, A.N.Clark, A.G.Hayes, J.D.Hall, R.Hume, D.A.Board, P.G.Smythe, M.L.Flanagan, J.U.

(2010) Eur.J.Med.Chem. 45: 447-454

  • DOI: 10.1016/j.ejmech.2009.10.025

  • PubMed Abstract: 
  • Prostaglandin D(2) synthesised by the hematopoietic prostaglandin D(2) synthase has a pro-inflammatory effect in allergic asthma, regulating many hallmark characteristics of the disease. Here we describe identification of hematopoietic prostaglandin ...

    Prostaglandin D(2) synthesised by the hematopoietic prostaglandin D(2) synthase has a pro-inflammatory effect in allergic asthma, regulating many hallmark characteristics of the disease. Here we describe identification of hematopoietic prostaglandin D(2) synthase inhibitors including cibacron blue, bromosulfophthalein and ethacrynic acid. Expansion around the drug-like ethacrynic acid identified a novel inhibitor, nocodazole, and a fragment representing its aromatic core. Nocodazole binding was further characterised by docking calculations in combination with conformational strain analysis. The benzyl thiophene core was predicted to be buried in the active site, binding in the putative prostaglandin binding site, and a likely hydrogen bond donor site identified. X-ray crystallographic studies supported the predicted binding mode.


    Organizational Affiliation

    The University of Queensland, Institute for Molecular Bioscience, Building 80, St Lucia, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione-requiring prostaglandin D synthase
A, B
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSH
Query on GSH

Download SDF File 
Download CCD File 
A
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
NZO
Query on NZO

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Download CCD File 
A
nocodazole
methyl [6-(thiophen-2-ylcarbonyl)-1H-benzimidazol-2-yl]carbamate
C14 H11 N3 O3 S
KYRVNWMVYQXFEU-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NZOIC50: ~65000 nM BINDINGMOAD
NZOIC50: 65000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.220α = 90.00
b = 79.359β = 90.00
c = 107.547γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-09-04 
  • Released Date: 2008-09-16 
  • Deposition Author(s): Oakley, A.J.

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-12-14
    Type: Non-polymer description
  • Version 1.3: 2017-10-25
    Type: Refinement description