5OX6

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Vadadustat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials.

Yeh, T.L.Leissing, T.M.Abboud, M.I.Thinnes, C.C.Atasoylu, O.Holt-Martyn, J.P.Zhang, D.Tumber, A.Lippl, K.Lohans, C.T.Leung, I.K.H.Morcrette, H.Clifton, I.J.Claridge, T.D.W.Kawamura, A.Flashman, E.Lu, X.Ratcliffe, P.J.Chowdhury, R.Pugh, C.W.Schofield, C.J.

(2017) Chem Sci 8: 7651-7668

  • DOI: 10.1039/c7sc02103h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophys ...

    Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The 'clinical' PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.


    Related Citations: 
    • Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain.
      Chan, M.C.,Atasoylu, O.,Hodson, E.,Tumber, A.,Leung, I.K.,Chowdhury, R.,Gomez-Perez, V.,Demetriades, M.,Rydzik, A.M.,Holt-Martyn, J.,Tian, Y.M.,Bishop, T.,Claridge, T.D.,Kawamura, A.,Pugh, C.W.,Ratcliffe, P.J.,Schofield, C.J.
      (2015) PLoS ONE 10: e0132004
    • 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


    Organizational Affiliation

    Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK.,The Francis Crick Institute , 1 Midland Road , London NW1 1AT , UK.,Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK . Email: christopher.schofield@chem.ox.ac.uk.,Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK.,Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK.,Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 1
A
252Homo sapiensMutation(s): 0 
Gene Names: EGLN1 (C1orf12)
EC: 1.14.11.29
Find proteins for Q9GZT9 (Homo sapiens)
Go to Gene View: EGLN1
Go to UniProtKB:  Q9GZT9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
A1Z
Query on A1Z

Download SDF File 
Download CCD File 
A
Vadadustat
GSK128863
C14 H11 Cl N2 O4
JGRXMPYUTJLTKT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A1ZIC50: 7 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 111.088α = 90.00
b = 111.088β = 90.00
c = 39.971γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references