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, mass spectrometry

Macromolecule Content

• Total Structure Weight: 20.40 kDa 
• Atom Count: 1444 
• Modelled Residue Count: 166 
• Deposited Residue Count: 170 
• Unique protein chains: 1

6ARK

Crystal Structure of compound 10 covalently bound to K-Ras G12C

• PDB DOI: 10.2210/pdb6ARK/pdb

• Classification: signaling protein/inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2017-08-22 Released: 2018-01-31 
• Deposition Author(s): Nnadi, C.I., Jenkins, M.L., Gentile, D.R., Bateman, L.A., Zaidman, D., Balius, T.E., Nomura, D.K., Burke, J.E., Shokat, K.M., London, N.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Israel Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.231 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange.

Nnadi, C.I., Jenkins, M.L., Gentile, D.R., Bateman, L.A., Zaidman, D., Balius, T.E., Nomura, D.K., Burke, J.E., Shokat, K.M., London, N.

(2018) J Chem Inf Model 58: 464-471

• PubMed: 29320178 
• DOI: 10.1021/acs.jcim.7b00399
• Primary Citation of Related Structures:  
  6ARK


• PubMed Abstract: 
  

The success of targeted covalent inhibitors in the global pharmaceutical industry has led to a resurgence of covalent drug discovery. However, covalent inhibitor design for flexible binding sites remains a difficult task due to a lack of methodological development. Here, we compared covalent docking to empirical electrophile screening against the highly dynamic target K-Ras ^G12C . While the overall hit rate of both methods was comparable, we were able to rapidly progress a docking hit to a potent irreversible covalent binder that modifies the inactive, GDP-bound state of K-Ras ^G12C . Hydrogen-deuterium exchange mass spectrometry was used to probe the protein dynamics of compound binding to the switch-II pocket and subsequent destabilization of the nucleotide-binding region. SOS-mediated nucleotide exchange assays showed that, contrary to prior switch-II pocket inhibitors, these new compounds appear to accelerate nucleotide exchange. This study highlights the efficiency of covalent docking as a tool for the discovery of chemically novel hits against challenging targets.

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Organizational Affiliation: 

Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	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	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
BQD (Subject of Investigation/LOI)	D [auth A]	(3R)-N-(6-bromonaphthalen-2-yl)-3-hydroxy-1-propanoyl-L-prolinamide C18 H19 Br N2 O3 MFZHXIHGHGFXNJ-WBVHZDCISA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.231 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.28	α = 90
b = 94.28	β = 90
c = 119.55	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-08-22 
• Released Date: 2018-01-31 
Deposition Author(s): Nnadi, C.I., Jenkins, M.L., Gentile, D.R., Bateman, L.A., Zaidman, D., Balius, T.E., Nomura, D.K., Burke, J.E., Shokat, K.M., London, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R01CA190408-03
Israel Science Foundation	Israel	1097/16
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1F30CA214015-01

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence