4EC0

Crystal structure of hH-PGDS with water displacing inhibitor

Structural Biology Knowledgebase: 4EC0 SBKB.org


Experimental Data Snapshot

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

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4EC0

Classification: isomerase / isomerase inhibitor

Total Structure Weight: 48046.84

Macromolecule Entities
Molecule Chains Length Organism Details
Hematopoietic prostaglandin D synthase A, B 200 Homo sapiens EC#: 5.3.99.2 IUBMB
Gene Name(s): HPGDS Gene View GSTS PGDS PTGDS2

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
7PQ
Query on 7PQ

A 4-[2-(aminomethyl)naphthalen-1-yl]-N-[2-(morpholin- 4-yl)ethyl]benzamide
C24 H27 N3 O2
LJXMOYXCVXIDDM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GSH
Query on GSH

A, B GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
7PQ IC50: 845 nM (100) BindingDB

N/A in BindingMoad
IC50: 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
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 48.74 α = 90.00
b = 77.71 β = 91.56
c = 52.45 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2013-01-02
    Type: Citation | Details: Citation update