5OCG

Discovery of small molecules binding to KRAS via high affinity antibody fragment competition method.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment.

Quevedo, C.E.Cruz-Migoni, A.Bery, N.Miller, A.Tanaka, T.Petch, D.Bataille, C.J.R.Lee, L.Y.W.Fallon, P.S.Tulmin, H.Ehebauer, M.T.Fernandez-Fuentes, N.Russell, A.J.Carr, S.B.Phillips, S.E.V.Rabbitts, T.H.

(2018) Nat Commun 9: 3169-3169

  • DOI: 10.1038/s41467-018-05707-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeting specific protein-protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibiti ...

    Targeting specific protein-protein interactions (PPIs) is an attractive concept for drug development, but hard to implement since intracellular antibodies do not penetrate cells and most small-molecule drugs are considered unsuitable for PPI inhibition. A potential solution to these problems is to select intracellular antibody fragments to block PPIs, use these antibody fragments for target validation in disease models and finally derive small molecules overlapping the antibody-binding site. Here, we explore this strategy using an anti-mutant RAS antibody fragment as a competitor in a small-molecule library screen for identifying RAS-binding compounds. The initial hits are optimized by structure-based design, resulting in potent RAS-binding compounds that interact with RAS inside the cells, prevent RAS-effector interactions and inhibit endogenous RAS-dependent signalling. Our results may aid RAS-dependent cancer drug development and demonstrate a general concept for developing small compounds to replace intracellular antibody fragments, enabling rational drug development to target validated PPIs.


    Organizational Affiliation

    Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A
189Homo sapiensMutation(s): 0 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9R5
Query on 9R5

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Download CCD File 
A
[(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine
C9 H10 Cl N O2
OGSHRCYGTQQEAO-SSDOTTSWSA-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
GNP
Query on GNP

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

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.175 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 78.085α = 90.00
b = 78.085β = 90.00
c = 77.650γ = 120.00
Software Package:
Software NamePurpose
EDNAdata collection
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-10-16
    Type: Data collection