4BQX

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.

Chowdhury, R.Candela-Lena, J.I.Chan, M.C.Greenald, D.J.Yeoh, K.K.Tian, Y.M.McDonough, M.A.Tumber, A.Rose, N.R.Conejo-Garcia, A.Demetriades, M.Mathavan, S.Kawamura, A.Lee, M.K.van Eeden, F.Pugh, C.W.Ratcliffe, P.J.Schofield, C.J.

(2013) ACS Chem Biol 8: 1488-1496

  • DOI: https://doi.org/10.1021/cb400088q
  • Primary Citation of Related Structures:  
    4BQW, 4BQX, 4BQY

  • PubMed Abstract: 

    The hypoxia inducible factor (HIF) system is central to the signaling of low oxygen (hypoxia) in animals. The levels of HIF-α isoforms are regulated in an oxygen-dependent manner by the activity of the HIF prolyl-hydroxylases (PHD or EGLN enzymes), which are Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. Here, we describe biochemical, crystallographic, cellular profiling, and animal studies on PHD inhibitors including selectivity studies using a representative set of human 2OG oxygenases. We identify suitable probe compounds for use in studies on the functional effects of PHD inhibition in cells and in animals.


  • Organizational Affiliation

    Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford, OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EGL NINE HOMOLOG 1252Homo sapiensMutation(s): 0 
EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9
GTEx:  ENSG00000135766 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UN9
Query on UN9

Download Ideal Coordinates CCD File 
C [auth A]N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE
C12 H9 Cl N2 O4
OUQVKRKGTAUJQA-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UN9 BindingDB:  4BQX Kd: 80 (nM) from 1 assay(s)
IC50: min: 70, max: 7500 (nM) from 8 assay(s)
EC50: 7.90e+4 (nM) from 1 assay(s)
PDBBind:  4BQX IC50: 300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.6α = 90
b = 109.6β = 90
c = 39.33γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.6: 2024-10-09
    Changes: Structure summary