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



Entry History 

Deposition Data

Revision History 

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