5UQW

Crystal structure of human KRAS G12V mutant in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Multivalent Small-Molecule Pan-RAS Inhibitors.

Welsch, M.E.Kaplan, A.Chambers, J.M.Stokes, M.E.Bos, P.H.Zask, A.Zhang, Y.Sanchez-Martin, M.Badgley, M.A.Huang, C.S.Tran, T.H.Akkiraju, H.Brown, L.M.Nandakumar, R.Cremers, S.Yang, W.S.Tong, L.Olive, K.P.Ferrando, A.Stockwell, B.R.

(2017) Cell 168: 878-889.e29

  • DOI: 10.1016/j.cell.2017.02.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-mole ...

    Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.


    Organizational Affiliation

    Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA.,Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY 10032, USA.,Department of Chemistry, Columbia University, New York, NY 10027, USA.,Department of Biological Sciences, St. John's University, Queens, NY 11439, USA.,Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Quantitative Proteomics and Metabolomics Center, Columbia University, New York, NY 10027, USA.,Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: bstockwell@columbia.edu.,Department of Pathology, Columbia University Medical Center, New York, NY 10032, USA; Division of Digestive and Liver Diseases in the Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
189Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.117 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 84.344α = 90.00
b = 84.344β = 90.00
c = 41.809γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence