4EDY | pdb_00004edy

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 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4EDY

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: https://doi.org/10.1016/j.bmcl.2012.04.004
  • Primary Citation 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. 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

Macromolecule Content 

  • Total Structure Weight: 47.86 kDa 
  • Atom Count: 4,021 
  • Modeled Residue Count: 395 
  • Deposited Residue Count: 398 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hematopoietic prostaglandin D synthase
A, B
199Homo 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
GTEx:  ENSG00000163106 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60760
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9PQ

Query on 9PQ



Download:Ideal Coordinates CCD File
E [auth A]4-[2-(hydroxymethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide
C24 H26 N2 O3
QFHPEAOPPKNNMS-UHFFFAOYSA-N
GSH

Query on GSH



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
F [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.204 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-01-02
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations