Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.07 kDa 
• Atom Count: 3422 
• Modelled Residue Count: 336 
• Deposited Residue Count: 340 
• Unique protein chains: 1

5V9U

Crystal Structure of small molecule ARS-1620 covalently bound to K-Ras G12C

• PDB DOI: 10.2210/pdb5V9U/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-03-23 Released: 2018-02-07 
• Deposition Author(s): Janes, M.R., Zhang, J., Li, L.-S., Hansen, R., Peters, U., Guo, X., Chen, Y., Babbar, A., Firdaus, S.J., Feng, J., Chen, J.H., Li, S., Brehmer, D., Darjania, L., Li, S., Long, Y.O., Thach, C., Liu, Y., Zarieh, A., Ely, T., Kucharski, J.M., Kessler, L.V., Wu, T., Wang, Y., Yao, Y., Deng, X., Zarrinkar, P., Dashyant, D., Lorenzi, M.V., Hu-Lowe, D., Patricelli, M.P., Ren, P., Liu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.189 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor.

Janes, M.R., Zhang, J., Li, L.S., Hansen, R., Peters, U., Guo, X., Chen, Y., Babbar, A., Firdaus, S.J., Darjania, L., Feng, J., Chen, J.H., Li, S., Li, S., Long, Y.O., Thach, C., Liu, Y., Zarieh, A., Ely, T., Kucharski, J.M., Kessler, L.V., Wu, T., Yu, K., Wang, Y., Yao, Y., Deng, X., Zarrinkar, P.P., Brehmer, D., Dhanak, D., Lorenzi, M.V., Hu-Lowe, D., Patricelli, M.P., Ren, P., Liu, Y.

(2018) Cell 172: 578-589.e17

• PubMed: 29373830 
• DOI: 10.1016/j.cell.2018.01.006
• Primary Citation of Related Structures:  
  5V9U


• PubMed Abstract: 
  

KRAS ^G12C was recently identified to be potentially druggable by allele-specific covalent targeting of Cys-12 in vicinity to an inducible allosteric switch II pocket (S-IIP). Success of this approach requires active cycling of KRAS ^G12C between its active-GTP and inactive-GDP conformations as accessibility of the S-IIP is restricted only to the GDP-bound state. This strategy proved feasible for inhibiting mutant KRAS in vitro; however, it is uncertain whether this approach would translate to in vivo. Here, we describe structure-based design and identification of ARS-1620, a covalent compound with high potency and selectivity for KRAS ^G12C . ARS-1620 achieves rapid and sustained in vivo target occupancy to induce tumor regression. We use ARS-1620 to dissect oncogenic KRAS dependency and demonstrate that monolayer culture formats significantly underestimate KRAS dependency in vivo. This study provides in vivo evidence that mutant KRAS can be selectively targeted and reveals ARS-1620 as representing a new generation of KRAS ^G12C -specific inhibitors with promising therapeutic potential.

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Organizational Affiliation: 

Wellspring Biosciences, San Diego, CA, USA; Kura Oncology, San Diego, CA, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B	170	Homo sapiens	Mutation(s): 4  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	H [auth A], P [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
91S	F [auth A], M [auth B]	(S)-1-{4-[6-chloro-8-fluoro-7-(2-fluoro-6-hydroxyphenyl)quinazolin-4-yl] piperazin-1-yl}propan-1-one C21 H19 Cl F2 N4 O2 ICXZXYUITXWHGD-UHFFFAOYSA-N
GOL	G [auth A], J [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], I [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.189 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.44	α = 77.48
b = 39.74	β = 81.97
c = 61.78	γ = 77.2

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-23 
• Released Date: 2018-02-07 
Deposition Author(s): Janes, M.R., Zhang, J., Li, L.-S., Hansen, R., Peters, U., Guo, X., Chen, Y., Babbar, A., Firdaus, S.J., Feng, J., Chen, J.H., Li, S., Brehmer, D., Darjania, L., Li, S., Long, Y.O., Thach, C., Liu, Y., Zarieh, A., Ely, T., Kucharski, J.M., Kessler, L.V., Wu, T., Wang, Y., Yao, Y., Deng, X., Zarrinkar, P., Dashyant, D., Lorenzi, M.V., Hu-Lowe, D., Patricelli, M.P., Ren, P., Liu, Y.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release