4XT2

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Isoform-Selective and Stereoselective Inhibition of Hypoxia Inducible Factor-2.

Scheuermann, T.H., Stroud, D., Sleet, C.E., Bayeh, L., Shokri, C., Wang, H., Caldwell, C.G., Longgood, J., MacMillan, J.B., Bruick, R.K., Gardner, K.H., Tambar, U.K.

(2015) J.Med.Chem. 58: 5930-5941

  • DOI: 10.1021/acs.jmedchem.5b00529

  • PubMed Abstract: 

    • Hypoxia inducible factor (HIF) transcription factors reside at the center of signaling pathways used by mammalian cells to sense and respond to low oxygen levels. While essential to maintain oxygen homeostasis, misregulation of HIF protein activity c ...

    Hypoxia inducible factor (HIF) transcription factors reside at the center of signaling pathways used by mammalian cells to sense and respond to low oxygen levels. While essential to maintain oxygen homeostasis, misregulation of HIF protein activity correlates with tumor development and metastasis. To provide artificial routes to target misregulated HIF activity, we identified small molecule antagonists of the HIF-2 transcription factor that bind an internal cavity within the C-terminal PAS domain of the HIF-2α subunit. Here we describe a new class of chiral small molecule ligands that provide the highest affinity binding, the most effective, isoform-selective inhibition of HIF-2 in cells, and trigger the largest protein conformation changes reported to date. The current results further illuminate the molecular mechanism of HIF-2 antagonism and suggest additional routes to develop higher affinity and potency HIF-2 antagonists.

    Organizational Affiliation: 

    †Department of Biophysics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aryl hydrocarbon receptor nuclear translocator
B, D
121Homo sapiensMutation(s): 1 
Gene Names: ARNT (BHLHE2)
Find proteins for P27540 (Homo sapiens)
Go to Gene View: ARNT
Go to UniProtKB:  P27540
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Endothelial PAS domain-containing protein 1
A, C
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
43L
Query on 43L
Download SDF File 
Download CCD File 
A, C
(5S,7R)-5,7-bis(3-bromophenyl)-4,5,6,7-tetrahydrotetrazolo[1,5-a]pyrimidine
C16 H13 Br2 N5
JHRYBPMSBXHLJL-LSDHHAIUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.698 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.253α = 90.00
b = 84.390β = 104.39
c = 82.784γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of TexasUnited StatesRP130513
National Institutes of Health/National Cancer InstituteUnited StatesP01 CA95471
Cancer Prevention and Research Institute of TexasUnited StatesRP100846

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-23
    Type: Refinement description
  • Version 1.2: 2017-09-06
    Type: Advisory, Author supporting evidence, Derived calculations