5OX5

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with CCT6, a GSK1278863-related compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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
  • Structures With Same Primary Citation

  • 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: 
    • 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
    • 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

    Organizational Affiliation

    Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK . Email: christopher.schofield@chem.ox.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egl nine homolog 1A252Homo sapiensMutation(s): 0 
Gene Names: EGLN1C1orf12PNAS-118PNAS-137
EC: 1.14.11.29
Find proteins for Q9GZT9 (Homo sapiens)
Explore Q9GZT9 
Go to UniProtKB:  Q9GZT9
NIH Common Fund Data Resources
PHAROS  Q9GZT9
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B2E
Query on B2E

Download CCD File 
A
(6-hydroxy-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbonyl)glycine
C9 H11 N3 O6
FFGCBWXERBBRBA-UHFFFAOYSA-N
 Ligand Interaction
BCT
Query on BCT

Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 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 %)
B2EIC50:  2600   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.147α = 90
b = 110.147β = 90
c = 39.368γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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