6GOF

KRAS full length G12D GPPNHP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds.

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

(2019) Proc. Natl. Acad. Sci. U.S.A. 116: 2545-2550

  • DOI: 10.1073/pnas.1811360116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The <i>RAS </i> gene family is frequently mutated in human cancers, and the quest for compounds that bind to mutant RAS remains a major goal, as it also does for inhibitors of protein-protein interactions. We have refined crystallization conditions ...

    The RAS gene family is frequently mutated in human cancers, and the quest for compounds that bind to mutant RAS remains a major goal, as it also does for inhibitors of protein-protein interactions. We have refined crystallization conditions for KRAS 169 Q61H -yielding crystals suitable for soaking with compounds and exploited this to assess new RAS-binding compounds selected by screening a protein-protein interaction-focused compound library using surface plasmon resonance. Two compounds, referred to as PPIN-1 and PPIN-2, with related structures from 30 initial RAS binders showed binding to a pocket where compounds had been previously developed, including RAS effector protein-protein interaction inhibitors selected using an intracellular antibody fragment (called Abd compounds). Unlike the Abd series of RAS binders, PPIN-1 and PPIN-2 compounds were not competed by the inhibitory anti-RAS intracellular antibody fragment and did not show any RAS-effector inhibition properties. By fusing the common, anchoring part from the two new compounds with the inhibitory substituents of the Abd series, we have created a set of compounds that inhibit RAS-effector interactions with increased potency. These fused compounds add to the growing catalog of RAS protein-protein inhibitors and show that building a chemical series by crossing over two chemical series is a strategy to create RAS-binding small molecules.


    Organizational Affiliation

    Chemistry Research Laboratory, University of Oxford, OX1 3TA Oxford, United Kingdom.,Department of Biochemistry, University of Oxford, OX1 3QU Oxford, United Kingdom.,Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom.,Research Complex at Harwell, Rutherford Appleton Laboratory, OX11 0FA Didcot, United Kingdom.,Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, John Radcliffe Hospital, University of Oxford, OX3 9DS Oxford, United Kingdom; terence.rabbitts@imm.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A
172Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.178 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 78.630α = 90.00
b = 78.630β = 90.00
c = 77.540γ = 120.00
Software Package:
Software NamePurpose
xia2data scaling
xia2data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references