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 

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Ligand Structure Quality Assessment 


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

  • 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. 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA [auth B],
C,
D,
E,
F		172Homo sapiensMutation(s): 1 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasB [auth A]172Homo sapiensMutation(s): 1 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1Z
Query on D1Z
Download Ideal Coordinates CCD File 
I [auth B],
J [auth A],
O [auth C],
T [auth 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 
H [auth B],
L [auth A],
N [auth C],
P [auth D],
S [auth E],
H [auth B],
L [auth A],
N [auth C],
P [auth D],
S [auth E],
V [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
W [auth F]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth B],
K [auth A],
M [auth C],
Q [auth D],
R [auth E],
G [auth B],
K [auth A],
M [auth C],
Q [auth D],
R [auth E],
U [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO		A [auth B],
C,
D,
E,
F		L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding Affinity
D1Z Binding MOAD:  6FA3 Kd: 38 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

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