3KXO

An orally active inhibitor bound at the active site of HPGDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione-requiring prostaglandin D synthase
A, B
202Homo 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
GSH
Query on GSH

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

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Download CCD File 
A, B
6-(3-fluorophenyl)-N-[1-(2,2,2-trifluoroethyl)piperidin-4-yl]pyridine-3-carboxamide
C19 H19 F4 N3 O
LPUCBGGXXIUBAZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KXOKd: 9.5 - 20 nM (100) BINDINGDB
KXOIC50: 200 nM (100) BINDINGDB
KXOEC50: 35 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.799α = 90.00
b = 78.364β = 91.61
c = 52.455γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACphasing
MAR345data collection
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Non-polymer description
  • Version 1.3: 2017-11-01
    Type: Refinement description