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.

doi:10.2210/pdb6gqx/pdb

Macromolecule Content

Total Structure Weight: 121247.42
Atom Count: 8082
Residue Count: 1025
Unique protein chains: 2

6GQX

KRAS-169 Q61H GPPNHP + CH-2

DOI: 10.2210/pdb6GQX/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): 2

Deposited: 2018-06-08 Released: 2019-02-06
Deposition Author(s): Cruz-Migoni, A., Quevedo, C.E., Carr, S.B., Phillips, S.E.V., Rabbitts, T.H.
Funding Organization(s): Wellcome Trust; Bloodwise; Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.230
R-Value Work: 0.202

wwPDB Validation3D 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

PubMed: 30683716 Search on PubMed
Primary Citation of Related Structures:
6GQY, 6GQW, 6GQT, 6GOM, 6GOG, 6GOF, 6GOE, 6GOD

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GTPase KRas	A, C, D, E, F	171	Homo sapiens	Mutation(s): 1 Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens) Go to Gene View: KRAS Go to UniProtKB: P01116
Protein Feature View Full Protein Feature View for P01116

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
GTPase KRas	B	170	Homo sapiens	Mutation(s): 1 Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens) Go to Gene View: KRAS Go to UniProtKB: P01116
Protein Feature View Full Protein Feature View for P01116

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
F8K Query on F8K Download SDF File Download CCD File	A, B, C	[4-[[2-methoxy-4-(3-methoxyphenyl)phenyl]amino]phenyl]methyl-dimethyl-azanium C₂₃ H₂₇ N₂ O₂ SVFQGOYYBWCBTN-UHFFFAOYSA-O		Ligand Interaction
MG Query on MG Download SDF File Download CCD File	A, B, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
GNP Query on GNP Download SDF File Download CCD File	A, B, C, D, E, F	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.230
R-Value Work: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 63.187	α = 90.00
b = 118.032	β = 90.00
c = 156.371	γ = 90.00

Software Package:

Software Name	Purpose
xia2	data reduction
PHASER	phasing
REFMAC	refinement
xia2	data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History & Funding Information

Deposition Data

Deposited Date: 2018-06-08
Released Date: 2019-02-06
Deposition Author(s): Cruz-Migoni, A., Quevedo, C.E., Carr, S.B., Phillips, S.E.V., Rabbitts, T.H.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	099246/Z/12/Z
Bloodwise	United Kingdom	12051
Medical Research Council (United Kingdom)	United Kingdom	MR/J000612/1

Revision History

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

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Deposition Help & Resources

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6GQX

KRAS-169 Q61H GPPNHP + CH-2

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

Entity ID: 1

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History