6FA3

Antibody derived (Abd-6) small molecule binding to KRAS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report



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:  
    5OCG, 5OCT, 5OCO, 6FA2, 6FA1, 6FA4, 6FA3

  • 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 inhibition. ...

    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. terence.rabbitts@imm.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRas BCDEF172Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS:  P01116
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRas A172Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS:  P01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1Z
Query on D1Z

Download Ideal Coordinates CCD File 
A, B, C, F
~{N}-[[(3~{R})-5-[5-[[3-[(dimethylamino)methyl]phenyl]amino]-6-methoxy-pyridin-2-yl]-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]oxane-4-carboxamide
C30 H36 N4 O5
FZJOWQUOIQPJIY-HSZRJFAPSA-N
 Ligand Interaction
GNP
Query on GNP

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B,C,D,E,FL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D1ZKd:  38   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.39α = 90
b = 118.48β = 90
c = 156.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



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