5UFP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

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:  
    5UFP

  • 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 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 ...

    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

    Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1A115Homo sapiensMutation(s): 1 
Gene Names: EPAS1BHLHE73HIF2AMOP2PASD2
Find proteins for Q99814 (Homo sapiens)
Explore Q99814 
Go to UniProtKB:  Q99814
NIH Common Fund Data Resources
PHAROS:  Q99814
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocatorB117Homo sapiensMutation(s): 1 
Gene Names: ARNTBHLHE2
Find proteins for P27540 (Homo sapiens)
Explore P27540 
Go to UniProtKB:  P27540
NIH Common Fund Data Resources
PHAROS:  P27540
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
86D
Query on 86D

Download Ideal Coordinates CCD File 
C [auth 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: 1.90 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.379α = 90
b = 84.057β = 106.48
c = 41.472γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
DENZOdata reduction

Structure Validation

View Full Validation Report



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  (Full details and data files)

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