3KXO

An orally active inhibitor bound at the active site of HPGDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.222 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KXOClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione-requiring prostaglandin D synthase
A, B
202Homo sapiensMutation(s): 0 
Gene Names: PTGDS2PGDS
EC: 5.3.99.2 (PDB Primary Data), 2.5.1.18 (UniProt)
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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
KXO BindingDB:  3KXO Kd: min: 9.5, max: 20 (nM) from 2 assay(s)
IC50: 200 (nM) from 1 assay(s)
EC50: 35 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.799α = 90
b = 78.364β = 91.61
c = 52.455γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted KXOClick on this verticalbar to view detailsBest fitted GSHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-21
    Changes: Non-polymer description
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations