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: 40.58 kDa 
• Atom Count: 3260 
• Modelled Residue Count: 334 
• Deposited Residue Count: 340 
• Unique protein chains: 1

6B0V

Crystal Structure of small molecule ARS-107 covalently bound to K-Ras G12C

• PDB DOI: 10.2210/pdb6B0V/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-09-15 Released: 2018-05-16 
• Deposition Author(s): Hansen, R., Peters, U., Babbar, A., Chen, Y., Feng, J., Janes, M.R., Li, L.-S., Ren, P., Liu, Y., Zarrinkar, P.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

The reactivity-driven biochemical mechanism of covalent KRASG12Cinhibitors.

Hansen, R., Peters, U., Babbar, A., Chen, Y., Feng, J., Janes, M.R., Li, L.S., Ren, P., Liu, Y., Zarrinkar, P.P.

(2018) Nat Struct Mol Biol 25: 454-462

• PubMed: 29760531 
• DOI: 10.1038/s41594-018-0061-5
• Primary Citation of Related Structures:  
  6B0V, 6B0Y


• PubMed Abstract: 
  

Activating mutations in KRAS are among the most common tumor driver mutations. Until recently, KRAS had been considered undruggable with small molecules; the discovery of the covalent KRAS ^G12C inhibitors ARS-853 and ARS-1620 has demonstrated that it is feasible to inhibit KRAS with high potency in cells and animals. Although the biological activity of these inhibitors has been described, the biochemical mechanism of how the compounds achieve potent inhibition remained incompletely understood. We now show that the activity of ARS-853 and ARS-1620 is primarily driven by KRAS-mediated catalysis of the chemical reaction with Cys12 in human KRAS ^G12C , while the reversible binding affinity is weak, in the hundreds of micromolar or higher range. The mechanism resolves how an induced, shallow and dynamic pocket not expected to support high-affinity binding of small molecules can nevertheless be targeted with potent inhibitors and may be applicable to other targets conventionally considered undruggable.

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Organizational Affiliation: 

Wellspring Biosciences, Inc., San Diego, CA, USA. [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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	F [auth A], J [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
C8G (Subject of Investigation/LOI)	E [auth A], I [auth B]	1-[3-(4-{[(4,5-dichloro-2-hydroxyphenyl)amino]acetyl}piperazin-1-yl)azetidin-1-yl]propan-1-one C18 H24 Cl2 N4 O3 JZGAPYVXPKOQIL-UHFFFAOYSA-N
CA	C [auth A], D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.218 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.14	α = 77
b = 39.88	β = 81.24
c = 62.43	γ = 77.58

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-09-15 
• Released Date: 2018-05-16 
Deposition Author(s): Hansen, R., Peters, U., Babbar, A., Chen, Y., Feng, J., Janes, M.R., Li, L.-S., Ren, P., Liu, Y., Zarrinkar, P.P.

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-05-30
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.2: 2018-11-07
  Changes: Data collection, Database references