1YCI

Factor inhibiting HIF-1 alpha in complex with N-(carboxycarbonyl)-D-phenylalanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective inhibition of factor inhibiting hypoxia-inducible factor

McDonough, M.A.McNeill, L.A.Tilliet, M.Papamicael, C.A.Chen, Q.Y.Banerji, B.Hewitson, K.S.Schofield, C.J.

(2005) J.Am.Chem.Soc. 127: 7680-7681

  • DOI: 10.1021/ja050841b
  • Also Cited By: 2ILM

  • PubMed Abstract: 
  • A set of four non-heme iron(II) and 2-oxoglutarate-dependent enzymes catalyze the post-translational modification of a transcription factor, hypoxia inducible factor (HIF), that mediates the hypoxic response in animals. Hydroxylation of HIF both caus ...

    A set of four non-heme iron(II) and 2-oxoglutarate-dependent enzymes catalyze the post-translational modification of a transcription factor, hypoxia inducible factor (HIF), that mediates the hypoxic response in animals. Hydroxylation of HIF both causes its degradation and limits its activity. We describe how the use of structural data coupled to solid-phase synthesis led to the discovery of a selective inhibitor of one of the HIF hydroxylases. The inhibitor N-oxalyl-d-phenylalanine was shown to inhibit the HIF asparaginyl hydroxylase (FIH) but not a HIF prolyl hydroxylase. A crystal structure of the inhibitor complexed to FIH reveals that it binds in the 2OG and, likely, in the dioxygen binding site. The results will help to enable the modulation of the hypoxic response for the up-regulation of specific genes of biomedical importance, such as erythropoietin and vascular endothelial growth factor.


    Related Citations: 
    • Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha
      Elkins, J.M.,Hewitson, K.S.,McNeill, L.A.,Seibel, J.F.,Schlemminger, I.,Pugh, C.W.,Ratcliffe, P.J.,Schofield, C.J.
      (2003) J.Biol.Chem. 278: 1802


    Organizational Affiliation

    The Department of Chemistry and The Oxford Centre for Molecular Sciences, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypoxia-inducible factor 1 alpha inhibitor
A
349Homo sapiensGene Names: HIF1AN (FIH1)
EC: 1.14.11.n4, 1.14.11.30
Find proteins for Q9NWT6 (Homo sapiens)
Go to Gene View: HIF1AN
Go to UniProtKB:  Q9NWT6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
N-(CARBOXYCARBONYL)-D-PHENYLALANINE
C11 H11 N O5
ULQWGBCNOHBNDB-MRVPVSSYSA-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 %)
NDFKi: 83000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.853α = 90.00
b = 86.853β = 90.00
c = 150.519γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance