2W0X

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

• PDB DOI: https://doi.org/10.2210/pdb2W0X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-10-10 Released: 2009-11-24 
• Deposition Author(s): Conejo-Garcia, A., Lienard, B.M.R., Clifton, I.J., McDonough, M.A., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.262 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Starting Model: experimental

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

• PubMed: 20822901 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.032
• Primary Citation of Related Structures:  
  2W0X, 2WA3, 2WA4


• 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.93 kDa 
• Atom Count: 3,041 
• Modelled Residue Count: 342 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOXIA-INDUCIBLE FACTOR 1 ALPHA INHIBITOR	A	349	Homo sapiens	Mutation(s): 0  EC: 1.14.11.16 (PDB Primary Data), 1.14.11.30 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens) Explore Q9NWT6  Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6 GTEx:  ENSG00000166135

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PD2	C [auth A]	PYRIDINE-2,4-DICARBOXYLIC ACID C7 H5 N O4 MJIVRKPEXXHNJT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PD2	BindingDB:  2W0X	IC50: min: 1100, max: 8600 (nM) from 2 assay(s)
	PDBBind:  2W0X	IC50: 6.25e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.262 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.471	α = 90
b = 86.471	β = 90
c = 147.237	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-24 
Deposition Author(s): Conejo-Garcia, A., Lienard, B.M.R., Clifton, I.J., McDonough, M.A., Schofield, C.J.

Revision History  

• Version 1.0: 2009-11-24
  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: 2017-07-05
  Changes: Refinement description
• Version 1.4: 2018-02-21
  Changes: Database references, Structure summary
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description