6FA1

Antibody derived (Abd-4) small molecule binding to KRAS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

    Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0FA, UK.,Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.,Domainex, Chesterford Research Park, Little Chesterford, Saffron Walden, CB10 1XL, UK.,Oxford Drug Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford, OX3 7FZ, UK.,Chemistry Research Laboratory, 12 Mansfield Rd, Oxford, OX1 3TA, UK.,Institute of Biological, Environmental and Rural Sciences, University of Aberystwyth, Aberystwyth, SY23 3EB, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Leeds Institute for Molecular Medicine, St James University Hospital, Leeds, LS9 7TF, UK.,Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK.,Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK. terence.rabbitts@imm.ox.ac.uk.,Research & Development, Sanofi K.K., Tokyo Opera City Tower, 3-20-2, Nishi Shinjuku, Shinjuku-ku, Tokyo, 163-1488, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
B
173Homo 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
GTPase KRas
A, C, D, F
172Homo 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: 3
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
E
173Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D2Z
Query on D2Z

Download SDF File 
Download CCD File 
A, B, F
2-[4-[[(3~{R})-2,3-dihydro-1,4-benzodioxin-3-yl]methylcarbamoyl]phenoxy]ethyl-dimethyl-azanium
C20 H25 N2 O4
NBQTZYRRRDQNKE-QGZVFWFLSA-O
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.610α = 90.00
b = 118.600β = 90.00
c = 156.610γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
GDAdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom100842/z/12/z
Wellcome TrustUnited Kingdom099246/z/12/z
BloodwiseUnited Kingdom12051
Medical Research Council (United Kingdom)United KingdomMR/J000612/1

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release