5LBE

HIF prolyl hydroxylase 2 (PHD2/EGLN1) G294E variant in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/FG2216)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for oxygen degradation domain selectivity of the HIF prolyl hydroxylases.

Chowdhury, R.Leung, I.K.Tian, Y.M.Abboud, M.I.Ge, W.Domene, C.Cantrelle, F.X.Landrieu, I.Hardy, A.P.Pugh, C.W.Ratcliffe, P.J.Claridge, T.D.Schofield, C.J.

(2016) Nat Commun 7: 12673-12673

  • DOI: 10.1038/ncomms12673
  • Primary Citation of Related Structures:  
    5L9R, 5L9V, 5L9B, 5LA9, 5LBC, 5LBF, 5LBE, 5LBB, 5LAS, 5LB6, 5LAT

  • PubMed Abstract: 
  • The response to hypoxia in animals involves the expression of multiple genes regulated by the αβ-hypoxia-inducible transcription factors (HIFs). The hypoxia-sensing mechanism involves oxygen limited hydroxylation of prolyl residues in the N- and C-terminal oxygen-dependent degradation domains (NODD and CODD) of HIFα isoforms, as catalysed by prolyl hydroxylases (PHD 1-3) ...

    The response to hypoxia in animals involves the expression of multiple genes regulated by the αβ-hypoxia-inducible transcription factors (HIFs). The hypoxia-sensing mechanism involves oxygen limited hydroxylation of prolyl residues in the N- and C-terminal oxygen-dependent degradation domains (NODD and CODD) of HIFα isoforms, as catalysed by prolyl hydroxylases (PHD 1-3). Prolyl hydroxylation promotes binding of HIFα to the von Hippel-Lindau protein (VHL)-elongin B/C complex, thus signalling for proteosomal degradation of HIFα. We reveal that certain PHD2 variants linked to familial erythrocytosis and cancer are highly selective for CODD or NODD. Crystalline and solution state studies coupled to kinetic and cellular analyses reveal how wild-type and variant PHDs achieve ODD selectivity via different dynamic interactions involving loop and C-terminal regions. The results inform on how HIF target gene selectivity is achieved and will be of use in developing selective PHD inhibitors.


    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
    • Structural basis for binding of hypoxia-inducible factor to the oxygen-sensing prolyl hydroxylases.
      Chowdhury, R., McDonough, M.A., Mecinovic, J., Loenarz, C., Flashman, E., Hewitson, K.S., Domene, C., Schofield, C.J.
      (2009) Structure 17: 981

    Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Egl nine homolog 1A252Homo sapiensMutation(s): 1 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UN9 (Subject of Investigation/LOI)
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
 Ligand Interaction
BCT
Query on BCT

Download Ideal Coordinates CCD File 
D [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UN9 BindingDB:  5LBE 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)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.45α = 90
b = 110.45β = 90
c = 39.654γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2017-11-29
    Changes: Database references