5UFQ

K-RasG12D(GNP)/R11.1.6 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

An engineered protein antagonist of K-Ras/B-Raf interaction.

Kauke, M.J.Traxlmayr, M.W.Parker, J.A.Kiefer, J.D.Knihtila, R.McGee, J.Verdine, G.Mattos, C.Wittrup, K.D.

(2017) Sci Rep 7: 5831-5831

  • DOI: 10.1038/s41598-017-05889-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ras is at the hub of signal transduction pathways controlling cell proliferation and survival. Its mutants, present in about 30% of human cancers, are major drivers of oncogenesis and render tumors unresponsive to standard therapies. Here we report t ...

    Ras is at the hub of signal transduction pathways controlling cell proliferation and survival. Its mutants, present in about 30% of human cancers, are major drivers of oncogenesis and render tumors unresponsive to standard therapies. Here we report the engineering of a protein scaffold for preferential binding to K-Ras G12D. This is the first reported inhibitor to achieve nanomolar affinity while exhibiting specificity for mutant over wild type (WT) K-Ras. Crystal structures of the protein R11.1.6 in complex with K-Ras WT and K-Ras G12D offer insight into the structural basis for specificity, highlighting differences in the switch I conformation as the major defining element in the higher affinity interaction. R11.1.6 directly blocks interaction with Raf and reduces signaling through the Raf/MEK/ERK pathway. Our results support greater consideration of the state of switch I and provide a novel tool to study Ras biology. Most importantly, this work makes an unprecedented contribution to Ras research in inhibitor development strategy by revealing details of a targetable binding surface. Unlike the polar interfaces found for Ras/effector interactions, the K-Ras/R11.1.6 complex reveals an extensive hydrophobic interface that can serve as a template to advance the development of high affinity, non-covalent inhibitors of K-Ras oncogenic mutants.


    Organizational Affiliation

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115, USA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. wittrup@mit.edu.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. wittrup@mit.edu.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. wittrup@mit.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
166Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
R11.1.6
C, D
61N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.717α = 90.00
b = 42.707β = 113.33
c = 100.235γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PHENIXphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesMCB-1517295

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release