5KYK

Covalent GTP-competitive inhibitors of KRAS G12C: Guanosine bisphosphonate Analogs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.267 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Covalent Guanosine Mimetic Inhibitors of G12C KRAS.

Xiong, Y.Lu, J.Hunter, J.Li, L.Scott, D.Choi, H.G.Lim, S.M.Manandhar, A.Gondi, S.Sim, T.Westover, K.D.Gray, N.S.

(2017) ACS Med Chem Lett 8: 61-66

  • DOI: 10.1021/acsmedchemlett.6b00373

  • PubMed Abstract: 
  • Ras proteins are members of a large family of GTPase enzymes that are commonly mutated in cancer where they act as dominant oncogenes. We previously developed an irreversible guanosine-derived inhibitor, SML-8-73-1, of mutant G12C RAS that forms a co ...

    Ras proteins are members of a large family of GTPase enzymes that are commonly mutated in cancer where they act as dominant oncogenes. We previously developed an irreversible guanosine-derived inhibitor, SML-8-73-1, of mutant G12C RAS that forms a covalent bond with cysteine 12. Here we report exploration of the structure-activity relationships (SAR) of hydrolytically stable analogues of SML-8-73-1 as covalent G12C KRAS inhibitors. We report the discovery of difluoromethylene bisphosphonate analogues such as compound 11 , which, despite exhibiting reduced efficiency as covalent G12C KRAS inhibitors, remove the liability of the hydrolytic instability of the diphosphate moiety present in SML-8-73-1 and provide the foundation for development of prodrugs to facilitate cellular uptake. The SAR and crystallographic results reaffirm the exquisite molecular recognition that exists in the diphosphate region of RAS for guanosine nucleotides which must be considered in the design of nucleotide-competitive inhibitors.


    Organizational Affiliation

    Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea.,Departments of Biochemistry and Radiation Oncology, The University of Texas, Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States.,Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02115, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215, United States.,New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation , Daegu 41061, Republic of Korea.,Center for Neuro-Medicine, Korea Institute of Science and Technology , Seoul 02792, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B, C
169Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6ZD
Query on 6ZD

Download SDF File 
Download CCD File 
A, B, C
5'-O-[(R)-[({2-[(chloroacetyl)amino]ethyl}sulfamoyl)methyl](hydroxy)phosphoryl]guanosine
C15 H23 Cl N7 O10 P S
AYYURYDKBCGXDD-FRJWGUMJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.702 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.267 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.830α = 90.00
b = 66.155β = 112.98
c = 98.006γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
V Scholar ResearchUnited StatesWel I-1829

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release