6ARK

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acs.jcim.7b00399

  • 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 methodologic ...

    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.


    Organizational Affiliation

    Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco , San Francisco, California 94158, United States.,Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States.,Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States.,Department of Organic Chemistry, The Weizmann Institute of Science , Rehovot, 7610001, Israel.,Department of Biochemistry and Microbiology. University of Victoria , Victoria, BC V8W 2Y2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A
170Homo sapiensMutation(s): 4 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BQD
Query on BQD

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Download CCD File 
A
(3R)-N-(6-bromonaphthalen-2-yl)-3-hydroxy-1-propanoyl-L-prolinamide
C18 H19 Br N2 O3
MFZHXIHGHGFXNJ-WBVHZDCISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.194 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 94.280α = 90.00
b = 94.280β = 90.00
c = 119.550γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited States5R01CA190408-03
Israel Science FoundationIsrael1097/16
National Institutes of Health/National Cancer InstituteUnited States1F30CA214015-01

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references