5TBM

Crystal structure of PT2385 bound to HIF2a-B*:ARNT-B* complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Small-Molecule Antagonist of HIF2 alpha Is Efficacious in Preclinical Models of Renal Cell Carcinoma.

Wallace, E.M.Rizzi, J.P.Han, G.Wehn, P.M.Cao, Z.Du, X.Cheng, T.Czerwinski, R.M.Dixon, D.D.Goggin, B.S.Grina, J.A.Halfmann, M.M.Maddie, M.A.Olive, S.R.Schlachter, S.T.Tan, H.Wang, B.Wang, K.Xie, S.Xu, R.Yang, H.Josey, J.A.

(2016) Cancer Res 76: 5491-5500

  • DOI: https://doi.org/10.1158/0008-5472.CAN-16-0473
  • Primary Citation of Related Structures:  
    5TBM

  • PubMed Abstract: 

    More than 90% of clear cell renal cell carcinomas (ccRCC) exhibit inactivation of the von Hippel-Lindau (pVHL) tumor suppressor, establishing it as the major underlying cause of this malignancy. pVHL inactivation results in stabilization of the hypoxia-inducible transcription factors, HIF1α and HIF2α, leading to expression of a genetic program essential for the initiation and progression of ccRCC. Herein, we describe the potent, selective, and orally active small-molecule inhibitor PT2385 as a specific antagonist of HIF2α that allosterically blocks its dimerization with the HIF1α/2α transcriptional dimerization partner ARNT/HIF1β. PT2385 inhibited the expression of HIF2α-dependent genes, including VEGF-A, PAI-1, and cyclin D1 in ccRCC cell lines and tumor xenografts. Treatment of tumor-bearing mice with PT2385 caused dramatic tumor regressions, validating HIF2α as a pivotal oncogenic driver in ccRCC. Notably, unlike other anticancer agents that inhibit VEGF receptor signaling, PT2385 exhibited no adverse effect on cardiovascular performance. Thus, PT2385 represents a novel class of therapeutics for the treatment of RCC with potent preclincal efficacy as well as improved tolerability relative to current agents that target the VEGF pathway. Cancer Res; 76(18); 5491-500. ©2016 AACR.


  • Organizational Affiliation

    Peloton Therapeutics, Inc., Dallas, Texas. eli.wallace@pelotontx.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1115Homo sapiensMutation(s): 1 
Gene Names: EPAS1BHLHE73HIF2AMOP2PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens)
Explore Q99814 
Go to UniProtKB:  Q99814
GTEx:  ENSG00000116016 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99814
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocator117Homo sapiensMutation(s): 1 
Gene Names: ARNTBHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens)
Explore P27540 
Go to UniProtKB:  P27540
GTEx:  ENSG00000143437 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27540
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
79A
Query on 79A

Download Ideal Coordinates CCD File 
C [auth A]3-{[(1S)-2,2-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile
C17 H12 F3 N O4 S
ONBSHRSJOPSEGS-INIZCTEOSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
79A Binding MOAD:  5TBM Kd: 49 (nM) from 1 assay(s)
BindingDB:  5TBM IC50: min: 5, max: 17 (nM) from 4 assay(s)
EC50: min: 27, max: 158 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.4α = 90
b = 84.097β = 106.24
c = 41.401γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2016-09-21 
  • Deposition Author(s): Du, X.

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description