Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 28.09 kDa 
• Atom Count: 2150 
• Modelled Residue Count: 217 
• Deposited Residue Count: 238 
• Unique protein chains: 2

4GHI

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

• DOI: 10.2210/pdb4GHI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-08-07 Released: 2013-02-27 
• Deposition Author(s): Scheuermann, T.H., Key, J., Tambar, U.K., Bruick, R.K., Gardner, K.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

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

• PubMed: 23434853 
• DOI: 10.1038/nchembio.1185
• Primary Citation of Related Structures:  
  4GHI


• 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 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	A	117	Homo sapiens	Mutation(s): 1  Gene Names: BHLHE73, EPAS1, HIF2A, MOP2, PASD2
Find proteins for Q99814 (Homo sapiens) Explore Q99814  Go to UniProtKB:  Q99814
NIH Common Fund Data Resources
PHAROS:  Q99814 GTEx:  ENSG00000116016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	B	121	Homo sapiens	Mutation(s): 1  Gene Names: ARNT, BHLHE2
Find proteins for P27540 (Homo sapiens) Explore P27540  Go to UniProtKB:  P27540
NIH Common Fund Data Resources
PHAROS:  P27540 GTEx:  ENSG00000143437

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0X3	C [auth A]	N-(3-chloro-5-fluorophenyl)-4-nitro-2,1,3-benzoxadiazol-5-amine C12 H6 Cl F N4 O3 CDQUJZKBRAFWNG-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0X3	Kd:  81   nM  Binding MOAD
0X3	Kd :  81   nM  PDBBind
0X3	Kd:  90   nM  BindingDB
0X3	IC50:  490   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.196 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.353	α = 90
b = 83	β = 105.98
c = 41.02	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-07 
• Released Date: 2013-02-27 
Deposition Author(s): Scheuermann, T.H., Key, J., Tambar, U.K., Bruick, R.K., Gardner, K.H.

Revision History  

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