5UQW

Crystal structure of human KRAS G12V mutant in complex with GDP

• PDB DOI:  https://doi.org/10.2210/pdb5UQW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-08 Released: 2017-03-22 
• Deposition Author(s): Huang, C.S., Kaplan, A., Stockwell, B.R., Tong, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.153 
• R-Value Work: 0.117 
• R-Value Observed: 0.118 

Literature

Multivalent Small-Molecule Pan-RAS Inhibitors.

Welsch, M.E., Kaplan, A., Chambers, J.M., Stokes, M.E., Bos, P.H., Zask, A., Zhang, Y., Sanchez-Martin, M., Badgley, M.A., Huang, C.S., Tran, T.H., Akkiraju, H., Brown, L.M., Nandakumar, R., Cremers, S., Yang, W.S., Tong, L., Olive, K.P., Ferrando, A., Stockwell, B.R.

(2017) Cell 168: 878-889.e29

• PubMed: 28235199 
• DOI: https://doi.org/10.1016/j.cell.2017.02.006
• Primary Citation of Related Structures:  
  5UQW, 5US4, 5USJ


• PubMed Abstract: 
  

Design of small molecules that disrupt protein-protein interactions, including the interaction of RAS proteins and their effectors, may provide chemical probes and therapeutic agents. We describe here the synthesis and testing of potential small-molecule pan-RAS ligands, which were designed to interact with adjacent sites on the surface of oncogenic KRAS. One compound, termed 3144, was found to bind to RAS proteins using microscale thermophoresis, nuclear magnetic resonance spectroscopy, and isothermal titration calorimetry and to exhibit lethality in cells partially dependent on expression of RAS proteins. This compound was metabolically stable in liver microsomes and displayed anti-tumor activity in xenograft mouse cancer models. These findings suggest that pan-RAS inhibition may be an effective therapeutic strategy for some cancers and that structure-based design of small molecules targeting multiple adjacent sites to create multivalent inhibitors may be effective for some proteins.

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Organizational Affiliation: 

Department of Chemistry, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.91 kDa 
• Atom Count: 2,926 
• Modelled Residue Count: 323 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A, B	189	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5 (PDB Primary Data), 3.6.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.153 
• R-Value Work: 0.117 
• R-Value Observed: 0.118 
• Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.344	α = 90
b = 84.344	β = 90
c = 41.809	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-22 
Deposition Author(s): Huang, C.S., Kaplan, A., Stockwell, B.R., Tong, L.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence