2YC0

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH R-2-HYDROXYGLUTARATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

The oncometabolite 2-hydroxyglutarate inhibits histone lysine demethylases.

Chowdhury, R.Yeoh, K.K.Tian, Y.M.Hillringhaus, L.Bagg, E.A.Rose, N.R.Leung, I.K.Li, X.S.Woon, E.C.Yang, M.McDonough, M.A.King, O.N.Clifton, I.J.Klose, R.J.Claridge, T.D.Ratcliffe, P.J.Schofield, C.J.Kawamura, A.

(2011) EMBO Rep 12: 463-469

  • DOI: https://doi.org/10.1038/embor.2011.43
  • Primary Citation of Related Structures:  
    2YBK, 2YBP, 2YBS, 2YC0, 2YDE

  • PubMed Abstract: 

    Mutations in isocitrate dehydrogenases (IDHs) have a gain-of-function effect leading to R(-)-2-hydroxyglutarate (R-2HG) accumulation. By using biochemical, structural and cellular assays, we show that either or both R- and S-2HG inhibit 2-oxoglutarate (2OG)-dependent oxygenases with varying potencies. Half-maximal inhibitory concentration (IC(50)) values for the R-form of 2HG varied from approximately 25 μM for the histone N(ɛ)-lysine demethylase JMJD2A to more than 5 mM for the hypoxia-inducible factor (HIF) prolyl hydroxylase. The results indicate that candidate oncogenic pathways in IDH-associated malignancy should include those that are regulated by other 2OG oxygenases than HIF hydroxylases, in particular those involving the regulation of histone methylation.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR352Homo sapiensMutation(s): 0 
EC: 1.14.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6
GTEx:  ENSG00000166135 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2HG
Query on 2HG

Download Ideal Coordinates CCD File 
C [auth A](2R)-2-hydroxypentanedioic acid
C5 H8 O5
HWXBTNAVRSUOJR-GSVOUGTGSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2HG PDBBind:  2YC0 IC50: 1.50e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.794α = 90
b = 86.794β = 90
c = 147.759γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-21
    Changes: Database references
  • Version 1.4: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description