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 

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Ligand Structure Quality Assessment 


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:  
    4EC0, 4EDY, 4EDZ, 4EE0

  • 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 molecules bind to our inhibitors and the enzyme ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthaseA, B200Homo sapiensMutation(s): 0 
Gene Names: GSTSHPGDSPGDSPTGDS2
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60760 (Homo sapiens)
Explore O60760 
Go to UniProtKB:  O60760
PHAROS:  O60760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7PQ
Query on 7PQ

Download Ideal Coordinates CCD File 
E [auth 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 Ideal Coordinates CCD File 
C [auth A],
F [auth B]
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7PQ PDBBind:  4EC0 IC50: 845 (nM) from 1 assay(s)
BindingDB:  4EC0 IC50: 845 (nM) from 1 assay(s)
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 = 48.74α = 90
b = 77.706β = 91.561
c = 52.449γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
X-PLORphasing
X-PLORrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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