8V39

Crystal structure of active KRAS-G12C (GMPPNP-bound) in complex with BBO-8520


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 ?
  • R-Value Free: 0.312 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.270 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of BBO-8520, a first-in-class direct and covalent dual inhibitor of GTP-bound (ON) and GDP-bound (OFF) KRASG12C.

Maciag, A.E.Stice, J.P.Wang, B.Sharma, A.K.Chan, A.H.Lin, K.Singh, D.Dyba, M.Yang, Y.Setoodeh, S.Smith, B.P.Ju, J.H.Jeknic, S.Rabara, D.Zhang, Z.Larsen, E.K.Esposito, D.Denson, J.P.Ranieri, M.Meynardie, M.Mehdizadeh, S.Alexander, P.A.Abreu Blanco, M.Turner, D.M.Xu, R.Lightstone, F.C.Wong, K.K.Stephen, A.G.Wang, K.Simanshu, D.K.Sinkevicius, K.W.Nissley, D.V.Wallace, E.McCormick, F.Beltran, P.J.

(2024) Cancer Discov 

  • DOI: https://doi.org/10.1158/2159-8290.CD-24-0840
  • Primary Citation of Related Structures:  
    8V39, 8V3A

  • PubMed Abstract: 

    Approved inhibitors of KRASG12C prevent oncogenic activation by sequestering the inactive, GDP-bound (OFF) form rather than directly binding and inhibiting the active, GTP-bound (ON) form. This approach provides no direct target coverage of the active protein. Expectedly, adaptive resistance to KRASG12C (OFF)-only inhibitors is observed in association with increased expression and activity of KRASG12C(ON). To provide optimal KRASG12C target coverage, we have developed BBO-8520, a first-in-class, direct dual inhibitor of KRASG12C(ON) and (OFF) forms. BBO-8520 binds in the Switch-II/Helix3 pocket, covalently modifies the target cysteine and disables effector binding to KRASG12C(ON). BBO-8520 exhibits potent signaling inhibition in growth factor activated states where current (OFF)-only inhibitors demonstrate little measurable activity. In vivo, BBO-8520 demonstrates rapid target engagement and inhibition of signaling, resulting in durable tumor regression in multiple models, including those resistant to KRASG12C(OFF)-only inhibitors. BBO-8520 is in Phase 1 clinical trials in patients with KRASG12C non-small cell lung cancer (NSCLC).


  • Organizational Affiliation

    Frederick National Laboratory for Cancer Research, Frederick, MD, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B, C
170Homo sapiensMutation(s): 2 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116-2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y8N (Subject of Investigation/LOI)
Query on Y8N

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
BBO-8520 (bound form)
C35 H35 F6 N7 O2 S
DWYHZCOHGXYZHA-VHJOERAISA-N
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 ?
  • R-Value Free: 0.312 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.270 
  • Space Group: P 65 2 2
Unit Cell:
Length ( ? )Angle ( ? )
a = 115.96¦Á = 90
b = 115.96¦Â = 90
c = 180.5¦Ă = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHHSN261200800001E

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release
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