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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/embor.2011.43
  • Primary Citation of Related Structures:  

  • 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-oxoglutarat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR
A
352Homo sapiensMutation(s): 0 
Gene Names: HIF1AN (FIH1)
EC: 1.14.11.30, 1.14.11.n4
Find proteins for Q9NWT6 (Homo sapiens)
Go to Gene View: HIF1AN
Go to UniProtKB:  Q9NWT6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2HG
Query on 2HG

Download SDF File 
Download CCD File 
A
(2R)-2-hydroxypentanedioic acid
C5 H8 O5
HWXBTNAVRSUOJR-GSVOUGTGSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2HGIC50: 1500000 nM BINDINGMOAD
2HGIC50: 1500000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.794α = 90.00
b = 86.794β = 90.00
c = 147.759γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-02-21
    Type: Database references