4EC0

Crystal structure of hH-PGDS with water displacing inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EC0/pdb

• Classification: isomerase/isomerase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-26 Released: 2012-05-16 
• Deposition Author(s): Day, J.E., Thorarensen, A., Trujillo, J.I.

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Experimental Data Snapshot

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

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

• PubMed: 22546671 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Departments of Medicinal Chemistry, Pfizer Global Research and Development, Chesterfield, MO 63017, United States. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.05 kDa 
• Atom Count: 4,133 
• Modelled Residue Count: 399 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hematopoietic prostaglandin D synthase	A, B	200	Homo sapiens	Mutation(s): 0  Gene Names: GSTS, HPGDS, PGDS, PTGDS2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7PQ	E [auth A]	4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin-4-yl)ethyl]benzamide C24 H27 N3 O2 LJXMOYXCVXIDDM-UHFFFAOYSA-N
GSH	C [auth A], F [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7PQ	PDBBind:  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 = 48.74	α = 90
b = 77.706	β = 91.561
c = 52.449	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
X-PLOR	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Day, J.E., Thorarensen, A., Trujillo, J.I.

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations