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 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1021/cb400088q
  • Structures With Same Primary Citation

  • 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), w ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EGL NINE HOMOLOG 1
A
252Homo sapiensMutation(s): 0 
Gene Names: EGLN1C1orf12PNAS-118PNAS-137
EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
Find proteins for Q9GZT9 (Homo sapiens)
Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UN9
Query on UN9

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

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UN9IC50:  1400   nM  BindingDB
UN9IC50:  424   nM  BindingDB
UN9IC50 :  300   nM  PDBBind
UN9IC50:  3900   nM  BindingDB
UN9IC50:  300   nM  BindingDB
UN9IC50:  73   nM  BindingDB
UN9IC50:  70   nM  BindingDB
UN9Kd:  80   nM  BindingDB
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



Entry History 

Deposition Data

Revision History 

  • 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