8V3A | pdb_00008v3a

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

• PDB DOI: https://doi.org/10.2210/pdb8V3A/pdb

• Classification: ONCOPROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-27 Released: 2024-12-18 
• Deposition Author(s): Chan, A.H., Bratcher, D.R., Simanshu, D.K.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

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.

(2025) Cancer Discov 15: 578-594

• PubMed: 39642212 
• DOI: https://doi.org/10.1158/2159-8290.CD-24-0840
• Primary Citation 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).

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Organizational Affiliation: 
• Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
BridgeBio Oncology Therapeutics, South San Francisco, CA, United States.
NCI Ras Initiative, Cancer Research Tenchnology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, United States.
National Cancer Institute, Frederick, MD, United States.
New York University Langone Medical Center, new york, ny, United States.
New York University Langone Medical Center, New York, NY, United States.
NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
Lawrence Livermore National Laboratory, Livermore, CA, United States.
New York University Langone Medical Center, New York, ny, United States.
Frederick National Laboratory for Cancer Research, Frederick, United States.
BridgeBio (United States), Boston, MA, United States.
University of California, San Francisco, San Francisco, CA, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.12 kDa 
• Atom Count: 3,209 
• Modeled Residue Count: 338 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B	170	Homo sapiens	Mutation(s): 2  Gene Names: KRAS, KRAS2, RASK2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y8N (Subject of Investigation/LOI)	E [auth A], H [auth B]	BBO-8520 (bound form) C35 H35 F6 N7 O2 S DWYHZCOHGXYZHA-VHJOERAISA-N
GDP	C [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.68	α = 90
b = 101.77	β = 90
c = 118.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Chan, A.H., Bratcher, D.R., Simanshu, D.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	HHSN261200800001E

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release
  
• Version 1.1: 2025-03-12
  Changes: Database references