Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.12 kDa 
• Atom Count: 1488 
• Modelled Residue Count: 177 
• Deposited Residue Count: 189 
• Unique protein chains: 1

4DSU

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

• DOI: 10.2210/pdb4DSU/pdb

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


• Deposited: 2012-02-19 Released: 2012-04-04 
• Deposition Author(s): Oh, A., Maurer, T., Garrenton, L.S., Pitts, K., Anderson, D.J., Skelton, N.J., Fauber, B.P., Pan, B., Malek, S., Stokoe, D., Ludlam, M., Bowman, K.K., Wu, J., Giannetti, A.M., Starovasnik, M.A., Mellman, I., Jackson, P.K., Ruldolph, J., Fang, G., Wang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity.

Maurer, T., Garrenton, L.S., Oh, A., Pitts, K., Anderson, D.J., Skelton, N.J., Fauber, B.P., Pan, B., Malek, S., Stokoe, D., Ludlam, M.J., Bowman, K.K., Wu, J., Giannetti, A.M., Starovasnik, M.A., Mellman, I., Jackson, P.K., Rudolph, J., Wang, W., Fang, G.

(2012) Proc Natl Acad Sci U S A 109: 5299-5304

• PubMed: 22431598 
• DOI: 10.1073/pnas.1116510109
• Primary Citation of Related Structures:  
  4DST, 4DSU, 4DSN, 4DSO


• PubMed Abstract: 
  

The Ras gene is frequently mutated in cancer, and mutant Ras drives tumorigenesis. Although Ras is a central oncogene, small molecules that bind to Ras in a well-defined manner and exert inhibitory effects have not been uncovered to date. Through an NMR-based fragment screen, we identified a group of small molecules that all bind to a common site on Ras. High-resolution cocrystal structures delineated a unique ligand-binding pocket on the Ras protein that is adjacent to the switch I/II regions and can be expanded upon compound binding. Structure analysis predicts that compound-binding interferes with the Ras/SOS interactions. Indeed, selected compounds inhibit SOS-mediated nucleotide exchange and prevent Ras activation by blocking the formation of intermediates of the exchange reaction. The discovery of a small-molecule binding pocket on Ras with functional significance provides a new direction in the search of therapeutically effective inhibitors of the Ras oncoprotein.

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Organizational Affiliation: 

Structural Biology, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas, isoform 2B	A	189	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6 (PDB Primary Data), 3.6.5.2 (UniProt)
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS:  P01116 GTEx:  ENSG00000133703

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
BZI	D [auth A]	BENZIMIDAZOLE C7 H6 N2 HYZJCKYKOHLVJF-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BZI	Kd :  1500000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.203 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.553	α = 90
b = 79.553	β = 90
c = 78.055	γ = 120

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-19 
• Released Date: 2012-04-04 
Deposition Author(s): Oh, A., Maurer, T., Garrenton, L.S., Pitts, K., Anderson, D.J., Skelton, N.J., Fauber, B.P., Pan, B., Malek, S., Stokoe, D., Ludlam, M., Bowman, K.K., Wu, J., Giannetti, A.M., Starovasnik, M.A., Mellman, I., Jackson, P.K., Ruldolph, J., Fang, G., Wang, W.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references
• Version 1.2: 2012-06-06
  Changes: Database references