5UFP

Crystal structure of PT2399 bound to HIF2a-B*:ARNT-B* complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

On-target efficacy of a HIF-2 alpha antagonist in preclinical kidney cancer models.

Cho, H.Du, X.Rizzi, J.P.Liberzon, E.Chakraborty, A.A.Gao, W.Carvo, I.Signoretti, S.Bruick, R.K.Josey, J.A.Wallace, E.M.Kaelin, W.G.

(2016) Nature 539: 107-111

  • DOI: 10.1038/nature19795
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Clear cell renal cell carcinoma, the most common form of kidney cancer, is usually linked to inactivation of the pVHL tumour suppressor protein and consequent accumulation of the HIF-2α transcription factor (also known as EPAS1). Here we show that a ...

    Clear cell renal cell carcinoma, the most common form of kidney cancer, is usually linked to inactivation of the pVHL tumour suppressor protein and consequent accumulation of the HIF-2α transcription factor (also known as EPAS1). Here we show that a small molecule (PT2399) that directly inhibits HIF-2α causes tumour regression in preclinical mouse models of primary and metastatic pVHL-defective clear cell renal cell carcinoma in an on-target fashion. pVHL-defective clear cell renal cell carcinoma cell lines display unexpectedly variable sensitivity to PT2399, however, suggesting the need for predictive biomarkers to be developed to use this approach optimally in the clinic.


    Organizational Affiliation

    Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothelial PAS domain-containing protein 1
A
115Homo 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
117Homo 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
86D
Query on 86D

Download SDF File 
Download CCD File 
A
3-({(1S)-7-[(difluoromethyl)sulfonyl]-2,2-difluoro-1-hydroxy-2,3-dihydro-1H-inden-4-yl}oxy)-5-fluorobenzonitrile
C17 H10 F5 N O4 S
MXUSGDMIHGLCNC-HNNXBMFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.379α = 90.00
b = 84.057β = 106.48
c = 41.472γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-05 
  • Released Date: 2017-01-25 
  • Deposition Author(s): Du, X.
  • This entry supersedes: 5T0T

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description