4EDY

Crystal structure of hH-PGDS with water displacing inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Investigation of the binding pocket of human hematopoietic prostaglandin (PG) D2 synthase (hH-PGDS): a tale of two waters.

Trujillo, J.I.Kiefer, J.R.Huang, W.Day, J.E.Moon, J.Jerome, G.M.Bono, C.P.Kornmeier, C.M.Williams, M.L.Kuhn, C.Rennie, G.R.Wynn, T.A.Carron, C.P.Thorarensen, A.

(2012) Bioorg Med Chem Lett 22: 3795-3799

  • DOI: 10.1016/j.bmcl.2012.04.004
  • Primary Citation of Related Structures:  
    4EC0, 4EE0, 4EDY, 4EDZ

  • PubMed Abstract: 
  • The inhibition of hH-PGDS has been proposed as a potential target for the development of anti-allergic and anti-inflammatory drugs. Herein we describe our investigation of the binding pocket of this important enzyme and our observation that two water ...

    The inhibition of hH-PGDS has been proposed as a potential target for the development of anti-allergic and anti-inflammatory drugs. Herein we describe our investigation of the binding pocket of this important enzyme and our observation that two water molecules bind to our inhibitors and the enzyme. A series of compounds were prepared to the probe the importance of the water molecules in determining the binding affinity of the inhibitors to the enzyme. The study provides insight into the binding requirements for the design of potent hH-PGDS inhibitors.


    Organizational Affiliation

    Departments of Medicinal Chemistry, Pfizer Global Research and Development, Chesterfield, MO 63017, United States. john.i.trujillo@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthaseAB199Homo sapiensMutation(s): 0 
Gene Names: GSTSHPGDSPGDSPTGDS2
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
Find proteins for O60760 (Homo sapiens)
Explore O60760 
Go to UniProtKB:  O60760
NIH Common Fund Data Resources
PHAROS  O60760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9PQ
Query on 9PQ

Download CCD File 
A
4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
C24 H26 N2 O3
QFHPEAOPPKNNMS-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

Download CCD File 
A, B
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9PQIC50 :  1480   nM  PDBBind
9PQIC50:  1480   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.685α = 90
b = 78.099β = 91.74
c = 52.585γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references