5OX6 | pdb_00005ox6

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 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5OX6

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1039/c7sc02103h
  • Primary Citation Related Structures: 
    5OP6, 5OP8, 5OPC, 5OX5, 5OX6

  • 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, 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.


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

Macromolecule Content 

  • Total Structure Weight: 28.83 kDa 
  • Atom Count: 1,936 
  • Modeled Residue Count: 222 
  • Deposited Residue Count: 252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Egl nine homolog 1252Homo sapiensMutation(s): 0 
Gene Names: EGLN1C1orf12PNAS-118PNAS-137
EC: 1.14.11.29
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1Z

Query on A1Z



Download:Ideal Coordinates CCD File
C [auth A]Vadadustat
C14 H11 Cl N2 O4
JGRXMPYUTJLTKT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.088α = 90
b = 111.088β = 90
c = 39.971γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data 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: 2017-10-18
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary