5UFP | pdb_00005ufp

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

• PDB DOI: https://doi.org/10.2210/pdb5UFP/pdb
• Entry: 5UFP supersedes: 5T0T

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2017-01-05 Released: 2017-01-25 
• Deposition Author(s): Du, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

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

• PubMed: 27595393 
• DOI: https://doi.org/10.1038/nature19795
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.
Peloton Therapeutics, Inc., Dallas, Texas 75235, USA.
Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75235, USA.
Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.47 kDa 
• Atom Count: 1,853 
• Modeled Residue Count: 214 
• Deposited Residue Count: 232 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	A	115	Homo sapiens	Mutation(s): 1  Gene Names: EPAS1, BHLHE73, HIF2A, MOP2, PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens) Explore Q99814  Go to UniProtKB:  Q99814
PHAROS:  Q99814 GTEx:  ENSG00000116016

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	B	117	Homo sapiens	Mutation(s): 1  Gene Names: ARNT, BHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens) Explore P27540  Go to UniProtKB:  P27540
PHAROS:  P27540 GTEx:  ENSG00000143437

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
86D	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

Binding Affinity Annotations
ID	Source	Binding Affinity
86D	BindingDB:  5UFP	IC50: min: 5, max: 8 (nM) from 2 assay(s)
		EC50: min: 6, max: 233 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.379	α = 90
b = 84.057	β = 106.48
c = 41.472	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Refinement description
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references