6F76

Antibody derived (Abd-8) small molecule binding to KRAS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions.

Bery, N.Cruz-Migoni, A.Bataille, C.J.Quevedo, C.E.Tulmin, H.Miller, A.Russell, A.Phillips, S.E.Carr, S.B.Rabbitts, T.H.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.37122
  • Primary Citation of Related Structures:  
    6F76

  • PubMed Abstract: 

    The RAS family of proteins is amongst the most highly mutated in human cancers and has so far eluded drug therapy. Currently, much effort is being made to discover mutant RAS inhibitors and in vitro screening for RAS-binding drugs must be followed by cell-based assays. Here, we have developed a robust set of bioluminescence resonance energy transfer (BRET)-based RAS biosensors that enable monitoring of RAS-effector interaction inhibition in living cells. These include KRAS, HRAS and NRAS and a variety of different mutations that mirror those found in human cancers with the major RAS effectors such as CRAF, PI3K and RALGDS. We highlighted the utility of these RAS biosensors by showing a RAS-binding compound is a potent pan-RAS-effector interactions inhibitor in cells. The RAS biosensors represent a useful tool to investigate and characterize the potency of anti-RAS inhibitors in cells and more generally any RAS protein-protein interaction (PPI) in cells.


  • Organizational Affiliation

    MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas173Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
H [auth B]
K [auth A]
N [auth C]
P [auth D]
S [auth E]
H [auth B],
K [auth A],
N [auth C],
P [auth D],
S [auth E],
U [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
CVK
Query on CVK

Download Ideal Coordinates CCD File 
I [auth B],
L [auth A],
O [auth C],
V [auth F]
4-(2,3-dihydro-1,4-benzodioxin-5-yl)-~{N}-[3-[(dimethylamino)methyl]phenyl]-2-methoxy-aniline
C24 H26 N2 O3
LEFMIEUBWDMNAT-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth B]
J [auth A]
M [auth C]
Q [auth D]
R [auth E]
G [auth B],
J [auth A],
M [auth C],
Q [auth D],
R [auth E],
T [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.19α = 90
b = 118.424β = 90
c = 156.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2018-08-08
    Type: Initial release