9BFZ | pdb_00009bfz

Tri-complex of Compound-5, KRAS G12C, and CypA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.222 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.181 (Depositor) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BFZ

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Elironrasib (RMC-6291), a Potent and Orally Bioavailable, RAS(ON) G12C-Selective, Covalent Tricomplex Inhibitor for the Treatment of Patients with RAS G12C-Addicted Cancers.

Cregg, J.Pota, K.Tomlinson, A.C.A.Yano, J.Marquez, A.Liu, Y.Schulze, C.J.Seamon, K.J.Holderfield, M.Wei, X.Zhuang, Y.Yang, Y.C.Jiang, J.Huang, Y.Zhao, R.Ling, Y.Wang, Z.Flagella, M.Wang, Z.Singh, M.Knox, J.E.Nichols, R.Wildes, D.Smith, J.A.M.Koltun, E.S.Gill, A.L.

(2025) J Med Chem 68: 6041-6063

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02313
  • Primary Citation Related Structures: 
    9BFV, 9BFW, 9BFX, 9BFY, 9BFZ

  • PubMed Abstract: 

    The discovery of elironrasib (RMC-6291) represents a significant breakthrough in targeting the previously deemed undruggable GTP-bound, active KRAS G12C . To target the active state of RAS (RAS(ON)) directly, we have employed an innovative tri-complex inhibitor (TCI) modality involving formation of a complex with an inhibitor, the intracellular chaperone protein CypA, and the target protein KRAS G12C in its GTP-bound form. The resulting tri-complex inhibits oncogenic signaling, inducing tumor regressions across various preclinical models of KRAS G12C mutant human cancers. Here we report structure-guided medicinal chemistry efforts that led to the discovery of elironrasib, a potent, orally bioavailable, RAS(ON) G12C-selective, covalent, tri-complex inhibitor. The investigational agent elironrasib is currently undergoing phase 1 clinical trials (NCT05462717, NCT06128551, NCT06162221), with preliminary data indicating clinical activity in patients who had progressed on first-generation inactive state-selective KRAS G12C inhibitors.


  • Organizational Affiliation
    • Revolution Medicines, Inc., Redwood City, California 94063, United States.

Macromolecule Content 

  • Total Structure Weight: 77.88 kDa 
  • Atom Count: 6,466 
  • Modeled Residue Count: 668 
  • Deposited Residue Count: 672 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase KRasA [auth B],
B [auth A]
170Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A
C, D
166Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AOK
(Subject of Investigation/LOI)

Query on A1AOK



Download:Ideal Coordinates CCD File
G [auth B],
J [auth A]
(3R)-N-[(2S)-1-{[(1M,8R,10S,14S,21M)-22-ethyl-4-hydroxy-21-[2-(2-methoxyethyl)phenyl]-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name)
C52 H68 N6 O8
WSKJWPKYVOMLEY-UHFFFAOYSA-N
GNP

Query on GNP



Download:Ideal Coordinates CCD File
E [auth B],
H [auth A]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth B],
I [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.222 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.181 (Depositor) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.894α = 90
b = 48.168β = 93.88
c = 102.112γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references