4GHI

Crystal structure of the high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains in complex with a benzoxadiazole antagonist

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Allosteric inhibition of hypoxia inducible factor-2 with small molecules.

Scheuermann, T.H., Li, Q., Ma, H.W., Key, J., Zhang, L., Chen, R., Garcia, J.A., Naidoo, J., Longgood, J., Frantz, D.E., Tambar, U.K., Gardner, K.H., Bruick, R.K.

(2013) Nat.Chem.Biol. 9: 271-276

  • DOI: 10.1038/nchembio.1185

  • PubMed Abstract: 

    • Hypoxia inducible factors (HIFs) are heterodimeric transcription factors induced in many cancers where they frequently promote the expression of protumorigenic pathways. Though transcription factors are typically considered 'undruggable', the PAS-B d ...

    Hypoxia inducible factors (HIFs) are heterodimeric transcription factors induced in many cancers where they frequently promote the expression of protumorigenic pathways. Though transcription factors are typically considered 'undruggable', the PAS-B domain of the HIF-2α subunit contains a large cavity within its hydrophobic core that offers a unique foothold for small-molecule regulation. Here we identify artificial ligands that bind within this pocket and characterize the resulting structural and functional changes caused by binding. Notably, these ligands antagonize HIF-2 heterodimerization and DNA-binding activity in vitro and in cultured cells, reducing HIF-2 target gene expression. Despite the high sequence identity between HIF-2α and HIF-1α, these ligands are highly selective and do not affect HIF-1 function. These chemical tools establish the molecular basis for selective regulation of HIF-2, providing potential therapeutic opportunities to intervene in HIF-2-driven tumors, such as renal cell carcinomas.

    Organizational Affiliation: 

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelial PAS domain-containing protein 1
A
117Homo sapiensMutation(s): 1 
Gene Names: EPAS1 (BHLHE73, HIF2A, MOP2, PASD2)
Find proteins for Q99814 (Homo sapiens)
Go to Gene View: EPAS1
Go to UniProtKB:  Q99814
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor nuclear translocator
B
121Homo sapiensMutation(s): 1 
Gene Names: ARNT (BHLHE2)
Find proteins for P27540 (Homo sapiens)
Go to Gene View: ARNT
Go to UniProtKB:  P27540
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0X3
Query on 0X3
Download SDF File 
Download CCD File 
A
N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine
C12 H6 Cl F N4 O3
CDQUJZKBRAFWNG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0X3Kd: 90 nM (99) BINDINGDB
0X3Kd: 81 nM BINDINGMOAD
0X3Kd: 81 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.353α = 90.00
b = 83.000β = 105.98
c = 41.020γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-2000data reduction
PHENIXphasing
PHENIXmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references