2W0X

FACTOR INHIBITING HIF-1 ALPHA WITH PYRIDINE 2,4 DICARBOXYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for binding of cyclic 2-oxoglutarate analogues to factor-inhibiting hypoxia-inducible factor.

Conejo-Garcia, A.McDonough, M.A.Loenarz, C.McNeill, L.A.Hewitson, K.S.Ge, W.Lienard, B.M.Schofield, C.J.Clifton, I.J.

(2010) Bioorg. Med. Chem. Lett. 20: 6125-6128

  • DOI: 10.1016/j.bmcl.2010.08.032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aromatic analogues of the 2-oxoglutarate co-substrate of the hypoxia-inducible factor hydroxylases are shown to bind at the active site iron: Pyridine-2,4-dicarboxylate binds as anticipated with a single molecule chelating the iron in a bidentate man ...

    Aromatic analogues of the 2-oxoglutarate co-substrate of the hypoxia-inducible factor hydroxylases are shown to bind at the active site iron: Pyridine-2,4-dicarboxylate binds as anticipated with a single molecule chelating the iron in a bidentate manner. The binding mode of a hydroxamic acid analogue, at least in the crystalline state, is unusual because two molecules of the inhibitor are observed at the active site and partial displacement of the iron binding aspartyl residue was observed.


    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, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR
A
349Homo 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PD2
Query on PD2

Download SDF File 
Download CCD File 
A
PYRIDINE-2,4-DICARBOXYLIC ACID
C7 H5 N O4
MJIVRKPEXXHNJT-UHFFFAOYSA-N
 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 %)
PD2IC50: 625000 nM BINDINGMOAD
PD2IC50: 625000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.471α = 90.00
b = 86.471β = 90.00
c = 147.237γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-24
    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: 2017-07-05
    Type: Refinement description
  • Version 1.4: 2018-02-21
    Type: Database references, Structure summary