9Q31 | pdb_00009q31

RIP1 kinase domain in complex with GDC-8264


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Discovery of Clinical Candidate GDC-8264, a Novel, Potent and Selective RIP1 Inhibitor for Amelioration of Tissue Damage and the Treatment of Inflammatory Diseases.

Patel, S.Chen, H.Varfolomeev, E.Kwon, Y.Ramaswamy, S.Kohli, P.B.Quinn, J.G.Webster, J.D.Mao, J.Chen, Y.Fong, R.Demircioglu, F.E.Lupardus, P.Stivala, C.Hamilton, G.L.Siu, M.Sujatha-Bhaskar, S.Mohanan, V.Adedeji, A.O.Santagostino, S.F.Maher, J.McKenzie, B.Rothenberg, M.E.Johnson, A.Vucic, D.

(2025) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01891
  • Primary Citation of Related Structures:  
    9Q31, 9Q32

  • PubMed Abstract: 

    Receptor-interacting protein 1 (RIP1) is a critical regulator of inflammatory cell death induced by diverse stimuli including TNF family ligands and ischemic injury. As such, the inhibition of RIP1 with small molecule kinase inhibitors is predicted to ameliorate tissue damage and associated inflammation. A novel ketone class of RIP1 inhibitors was identified via a high-throughput screen followed by structure-based scaffold hopping. Subsequent optimization yielded clinical molecule GDC-8264 (compound 19 ), which has excellent target selectivity and druglike attributes for once-daily oral dosing. GDC-8264 is currently being tested in a Phase 2 trial for the prevention of cardiac surgery-associated acute kidney injury (CSA-AKI) in hopes of providing benefit for patients requiring cardio-pulmonary bypass at medium to high risk of developing CSA-AKI.


  • Organizational Affiliation
    • Department of Discovery Chemistry, Genentech, South San Francisco, California 94080, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-interacting serine/threonine-protein kinase 1
A, B
296Homo sapiensMutation(s): 4 
Gene Names: RIPK1RIPRIP1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens)
Explore Q13546 
Go to UniProtKB:  Q13546
PHAROS:  Q13546
GTEx:  ENSG00000137275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13546
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CNU (Subject of Investigation/LOI)
Query on A1CNU

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
cyclopropyl[(4R,5S,7S)-7-fluoro-5-phenyl-6,7-dihydro-5H-pyrrolo[1,2-b][1,2,4]triazol-2-yl]methanone
C15 H14 F N3 O
LMXPZWQVDDSYHH-RYUDHWBXSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
O [auth B],
P [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
TME
Query on TME

Download Ideal Coordinates CCD File 
M [auth B]PROPANE
C3 H8
ATUOYWHBWRKTHZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
Q [auth B],
R [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
S [auth B],
T [auth B],
U [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.368α = 90
b = 96.318β = 90
c = 127.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release