7RP2

Crystal structure of Kas G12C in complex with 2H11 CLAMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors.

Davies, C.W.Oh, A.J.Mroue, R.Steffek, M.Bruning, J.M.Xiao, Y.Feng, S.Jayakar, S.Chan, E.Arumugam, V.Uribe, S.C.Drummond, J.Frommlet, A.Lu, C.Franke, Y.Merchant, M.Koeppen, H.Quinn, J.G.Malhotra, S.Do, S.Gazzard, L.Purkey, H.E.Rudolph, J.Mulvihill, M.M.Koerber, J.T.Wang, W.Evangelista, M.

(2022) Nat Biotechnol 40: 769-778

  • DOI: https://doi.org/10.1038/s41587-021-01126-9
  • Primary Citation of Related Structures:  
    7MDP, 7RP2, 7RP3, 7RP4

  • PubMed Abstract: 

    Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRAS G12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRAS G12C covalent modification in vivo and can be used to investigate response heterogeneity to KRAS G12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRAS G12C switch II region (SWII) by stabilizing a specific conformation of KRAS G12C , thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.


  • Organizational Affiliation

    Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas170Homo sapiensMutation(s): 4 
Gene Names: KRASKRAS2RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin IgG heavy chainB [auth H]226Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
immunoglobulin IgG light chainC [auth I]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.918α = 90
b = 68.796β = 114.08
c = 101.002γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description