8G9Q

Tricomplex of Compound-1, KRAS G12C, and CypA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Chemical remodeling of a cellular chaperone to target the active state of mutant KRAS.

Schulze, C.J.Seamon, K.J.Zhao, Y.Yang, Y.C.Cregg, J.Kim, D.Tomlinson, A.Choy, T.J.Wang, Z.Sang, B.Pourfarjam, Y.Lucas, J.Cuevas-Navarro, A.Ayala-Santos, C.Vides, A.Li, C.Marquez, A.Zhong, M.Vemulapalli, V.Weller, C.Gould, A.Whalen, D.M.Salvador, A.Milin, A.Saldajeno-Concar, M.Dinglasan, N.Chen, A.Evans, J.Knox, J.E.Koltun, E.S.Singh, M.Nichols, R.Wildes, D.Gill, A.L.Smith, J.A.M.Lito, P.

(2023) Science 381: 794-799

  • DOI: https://doi.org/10.1126/science.adg9652
  • Primary Citation of Related Structures:  
    8G9P, 8G9Q

  • PubMed Abstract: 

    The discovery of small-molecule inhibitors requires suitable binding pockets on protein surfaces. Proteins that lack this feature are considered undruggable and require innovative strategies for therapeutic targeting. KRAS is the most frequently activated oncogene in cancer, and the active state of mutant KRAS is such a recalcitrant target. We designed a natural product-inspired small molecule that remodels the surface of cyclophilin A (CYPA) to create a neomorphic interface with high affinity and selectivity for the active state of KRAS G12C (in which glycine-12 is mutated to cysteine). The resulting CYPA:drug:KRAS G12C tricomplex inactivated oncogenic signaling and led to tumor regressions in multiple human cancer models. This inhibitory strategy can be used to target additional KRAS mutants and other undruggable cancer drivers. Tricomplex inhibitors that selectively target active KRAS G12C or multiple RAS mutants are in clinical trials now (NCT05462717 and NCT05379985).


  • Organizational Affiliation

    Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo 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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase AB [auth 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
GNP
Query on GNP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
YV6 (Subject of Investigation/LOI)
Query on YV6

Download Ideal Coordinates CCD File 
E [auth A]methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate
C24 H36 N4 O6 S
VHGYJBMAJUGDAM-ZJOUEHCJSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.159α = 90
b = 100.689β = 90
c = 47.776γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
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: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2023-08-30
    Changes: Database references
  • Version 2.0: 2024-10-23
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary