1YCI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    1YCI

  • 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 causes its degradation and limits its activity ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hypoxia-inducible factor 1 alpha inhibitorA349Homo sapiensMutation(s): 0 
Gene Names: HIF1ANFIH1
EC: 1.14.11.16 (PDB Primary Data), 1.14.11.30 (UniProt), 1.14.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDF (Subject of Investigation/LOI)
Query on NDF

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]N-(CARBOXYCARBONYL)-D-PHENYLALANINE
C11 H11 N O5
ULQWGBCNOHBNDB-MRVPVSSYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NDF PDBBind:  1YCI Ki: 8.30e+4 (nM) from 1 assay(s)
BindingDB:  1YCI Kd: 8.30e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.853α = 90
b = 86.853β = 90
c = 150.519γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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