9I64 | pdb_00009i64

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.214 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.203 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9I64

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Casdatifan, Part II: A Potent and Orally Bioavailable Inhibitor of Hypoxia Inducible Factor-2 alpha.

Mailyan, A.K.Mata, G.Beatty, J.W.Drew, S.L.Fournier, J.Yu, K.Gal, B.Kalisiak, J.Yan, X.Tran, A.Su, Y.Rosen, B.R.Jeffrey, J.L.Hardman, C.Epplin, M.Ginn, E.Sun, M.Chen, A.Fabila, P.Sivick, K.E.Schweickert, P.G.Piovesan, D.Meleza, C.Pham, A.T.Chen, P.Y.Jin, L.Walters, M.J.Walker, N.P.Kwon, H.J.Leleti, M.R.Powers, J.P.Lawson, K.V.

(2026) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c03724
  • Primary Citation Related Structures: 
    9I64

  • PubMed Abstract: 

    Hypoxia-inducible factor 2α (HIF-2α) is recognized as a key oncogenic driver in clear cell renal cell carcinoma (ccRCC), the most prevalent type of kidney cancer. Here, we describe the discovery of a highly potent and selective tetralin-based HIF-2α inhibitor, casdatifan ( 61 ), originating from previously identified tetrahydroquinolines reported in the Part 1 companion manuscript. Casdatifan demonstrates a potentially best-in-class clinical profile. In a healthy volunteer study (NCT05117554), casdatifan exhibited a favorable pharmacokinetic profile, with an approximate 24-h half-life suitable for once-daily oral administration. Casdatifan has shown promising clinical activity in the ARC-20 ccRCC platform study, both as monotherapy and in combination with the VEGFR tyrosine kinase inhibitor (TKI) cabozantinib. Currently, casdatifan is being evaluated in a Phase 3 trial in combination with cabozantinib (NCT07011719) in patients with advanced ccRCC.


  • Organizational Affiliation
    • Arcus Biosciences, Inc., Hayward, California 94545, United States.

Macromolecule Content 

  • Total Structure Weight: 27.2 kDa 
  • Atom Count: 2,129 
  • Modeled Residue Count: 215 
  • Deposited Residue Count: 228 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endothelial PAS domain-containing protein 1112Homo sapiensMutation(s): 0 
Gene Names: EPAS1BHLHE73HIF2AMOP2PASD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99814 (Homo sapiens)
Explore Q99814 
Go to UniProtKB:  Q99814
PHAROS:  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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Aryl hydrocarbon receptor nuclear translocator116Homo sapiensMutation(s): 0 
Gene Names: ARNTBHLHE2
UniProt & NIH Common Fund Data Resources
Find proteins for P27540 (Homo sapiens)
Explore P27540 
Go to UniProtKB:  P27540
PHAROS:  P27540
GTEx:  ENSG00000143437 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27540
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I0H
(Subject of Investigation/LOI)

Query on A1I0H



Download:Ideal Coordinates CCD File
C [auth A](5~{R},6~{S},8~{R})-3,5,6-tris(fluoranyl)-8-[(1~{S},2~{R})-2-fluoranyl-7-methylsulfonyl-1-oxidanyl-2,3-dihydro-1~{H}-inden-4-yl]-5,6,7,8-tetrahydronaphthalene-1-carbonitrile
C21 H17 F4 N O3 S
KHBHHNNBNHHGPE-VWMDDZALSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
D [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.214 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.203 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.693α = 90
b = 61.15β = 90
c = 91.32γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Database references