9BGH | pdb_00009bgh

Crystal structure of KRAS G12D in a transition state mimetic complex with CYPA and RMC-7977


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Pharmacological restoration of GTP hydrolysis by mutant RAS.

Cuevas-Navarro, A.Pourfarjam, Y.Hu, F.Rodriguez, D.J.Vides, A.Sang, B.Fan, S.Goldgur, Y.de Stanchina, E.Lito, P.

(2025) Nature 637: 224-229

  • DOI: https://doi.org/10.1038/s41586-024-08283-2
  • Primary Citation of Related Structures:  
    9BGH, 9BHO, 9BHP, 9BHQ, 9BI1, 9BI2

  • PubMed Abstract: 

    Approximately 3.4 million patients worldwide are diagnosed each year with cancers that have pathogenic mutations in one of three RAS proto-oncogenes (KRAS, NRAS and HRAS) 1,2 . These mutations impair the GTPase activity of RAS, leading to activation of downstream signalling and proliferation 3-6 . Long-standing efforts to restore the hydrolase activity of RAS mutants have been unsuccessful, extinguishing any consideration towards a viable therapeutic strategy 7 . Here we show that tri-complex inhibitors-that is, molecular glues with the ability to recruit cyclophilin A (CYPA) to the active state of RAS-have a dual mechanism of action: not only do they prevent activated RAS from binding to its effectors, but they also stimulate GTP hydrolysis. Drug-bound CYPA complexes modulate residues in the switch II motif of RAS to coordinate the nucleophilic attack on the γ-phosphate of GTP in a mutation-specific manner. RAS mutants that were most sensitive to stimulation of GTPase activity were more susceptible to treatment than mutants in which the hydrolysis could not be enhanced, suggesting that pharmacological stimulation of hydrolysis potentiates the therapeutic effects of tri-complex inhibitors for specific RAS mutants. This study lays the foundation for developing a class of therapeutics that inhibit cancer growth by stimulating mutant GTPase activity.


  • Organizational Affiliation

    Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase AA [auth B],
B [auth D]
166Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
UniProt
Find proteins for P62938 (Chlorocebus aethiops)
Explore P62938 
Go to UniProtKB:  P62938
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62938
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRasC [auth A],
D [auth C]
170Homo sapiensMutation(s): 1 
Gene Names: KRAS
EC: 3.6.5.2
Membrane Entity: Yes 
UniProt
Find proteins for P79800 (Meleagris gallopavo)
Explore P79800 
Go to UniProtKB:  P79800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79800
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZNI (Subject of Investigation/LOI)
Query on ZNI

Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]
(1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide
C47 H60 N8 O6 S
NBLZKEHVVJSAAY-VLXWOFRQSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
AF3
Query on AF3

Download Ideal Coordinates CCD File 
K [auth C]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.483α = 90
b = 81.787β = 90
c = 127.832γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ZNIClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2025-01-29
    Changes: Database references