4EC0

Crystal structure of hH-PGDS with water displacing inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hematopoietic prostaglandin D synthase
A, B
200Homo 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
7PQ
Query on 7PQ

Download SDF File 
Download CCD File 
A
4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
C24 H27 N3 O2
LJXMOYXCVXIDDM-UHFFFAOYSA-N
 Ligand Interaction
GSH
Query on GSH

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

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7PQIC50: 845 nM (100) BINDINGDB
7PQIC50: 845 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.740α = 90.00
b = 77.706β = 91.56
c = 52.449γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
PDB_EXTRACTdata extraction
MAR345dtbdata collection
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description