Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 40.86 kDa 
• Atom Count: 3086 
• Modelled Residue Count: 333 
• Deposited Residue Count: 340 
• Unique protein chains: 1

5V6V

Crystal structure of small molecule aziridine 3 covalently bound to K-Ras G12C

• PDB DOI: 10.2210/pdb5V6V/pdb

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


• Deposited: 2017-03-17 Released: 2017-06-28 
• Deposition Author(s): McGregor, L.M., Jenkins, M., Kerwin, C., Burke, J.E., Shokat, K.M.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.202 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes.

McGregor, L.M., Jenkins, M.L., Kerwin, C., Burke, J.E., Shokat, K.M.

(2017) Biochemistry 56: 3178-3183

• PubMed: 28621541 
• DOI: 10.1021/acs.biochem.7b00271
• Primary Citation of Related Structures:  
  5V6S, 5V6V


• PubMed Abstract: 
  

There is growing interest in reversible and irreversible covalent inhibitors that target noncatalytic amino acids in target proteins. With a goal of targeting oncogenic K-Ras variants (e.g., G12D) by expanding the types of amino acids that can be targeted by covalent inhibitors, we survey a set of electrophiles for their ability to label carboxylates. We functionalized an optimized ligand for the K-Ras switch II pocket with a set of electrophiles previously reported to react with carboxylates and characterized the ability of these compounds to react with model nucleophiles and oncogenic K-Ras proteins. Here, we report that aziridines and stabilized diazo groups preferentially react with free carboxylates over thiols. Although we did not identify a warhead that potently labels K-Ras G12D, we were able to study the interactions of many electrophiles with K-Ras, as most of the electrophiles rapidly label K-Ras G12C. We characterized the resulting complexes by crystallography, hydrogen/deuterium exchange, and differential scanning fluorimetry. Our results both demonstrate the ability of a noncatalytic cysteine to react with a diverse set of electrophiles and emphasize the importance of proper spatial arrangements between a covalent inhibitor and its intended nucleophile. We hope that these results can expand the range of electrophiles and nucleophiles of use in covalent protein modulation.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco , San Francisco, California 94158, United States.

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
8YA	F [auth A], M [auth B]	3-amino-1-{4-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl}propan-1-one C23 H23 Cl F N7 O VJDYKBMYNVLSKK-UHFFFAOYSA-N
GDP	C [auth A], H [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A], E [auth A], G [auth B], I [auth B], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.202 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.23	α = 77.34
b = 39.17	β = 81.44
c = 62.34	γ = 76.86

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-17 
• Released Date: 2017-06-28 
Deposition Author(s): McGregor, L.M., Jenkins, M., Kerwin, C., Burke, J.E., Shokat, K.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA190408
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence