5OCT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B, C, D, E
A, B, C, D, E, F
187Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
G [auth A]
K [auth B]
N [auth C]
Q [auth D]
U [auth E]
G [auth A],
K [auth B],
N [auth C],
Q [auth D],
U [auth E],
Y [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
9R5
Query on 9R5

Download Ideal Coordinates CCD File 
AA [auth F]
H [auth A]
L [auth B]
O [auth C]
R [auth D]
AA [auth F],
H [auth A],
L [auth B],
O [auth C],
R [auth D],
S [auth D],
V [auth E],
W [auth E],
Z [auth F]
[(2~{R})-6-chloranyl-2,3-dihydro-1,4-benzodioxin-2-yl]methanamine
C9 H10 Cl N O2
OGSHRCYGTQQEAO-SSDOTTSWSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
BA [auth F]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CA [auth F]
J [auth A]
M [auth B]
P [auth C]
T [auth D]
CA [auth F],
J [auth A],
M [auth B],
P [auth C],
T [auth D],
X [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.49α = 90
b = 118.45β = 90
c = 155.36γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description