Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 95.76 kDa 
• Atom Count: 7864 
• Modelled Residue Count: 802 
• Deposited Residue Count: 816 
• Unique protein chains: 3

6CUP

Ras:SOS:Ras in complex with a small molecule activator

• PDB DOI: 10.2210/pdb6CUP/pdb

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


• Deposited: 2018-03-26 Released: 2019-02-06 
• Deposition Author(s): Phan, J., Abbott, J., Fesik, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.174 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 

Literature

Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS.

Abbott, J.R., Patel, P.A., Howes, J.E., Akan, D.T., Kennedy, J.P., Burns, M.C., Browning, C.F., Sun, Q., Rossanese, O.W., Phan, J., Waterson, A.G., Fesik, S.W.

(2018) ACS Med Chem Lett 9: 941-946

• PubMed: 30258545 
• DOI: 10.1021/acsmedchemlett.8b00296
• Primary Citation of Related Structures:  
  6CUO, 6CUP, 6CUR


• PubMed Abstract: 
  

Proteins in the RAS family are important regulators of cellular signaling and, when mutated, can drive cancer pathogenesis. Despite considerable effort over the last 30 years, RAS proteins have proven to be recalcitrant therapeutic targets. One approach for modulating RAS signaling is to target proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report hit-to-lead studies on quinazoline-containing compounds that bind to SOS1 and activate nucleotide exchange on RAS. Using structure-based design, we refined the substituents attached to the quinazoline nucleus and built in additional interactions not present in the initial HTS hit. Optimized compounds activate nucleotide exchange at single-digit micromolar concentrations in vitro. In HeLa cells, these quinazolines increase the levels of RAS-GTP and cause signaling changes in the mitogen-activated protein kinase/extracellular regulated kinase (MAPK/ERK) pathway.

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Related Citations: 

• Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
  Burns, M.C., Sun, Q., Daniels, R.N., Camper, D., Kennedy, J.P., Phan, J., Olejniczak, E.T., Lee, T., Waterson, A.G., Rossanese, O.W., Fesik, S.W.
  (2014) Proc Natl Acad Sci U S A 111: 3401

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Organizational Affiliation: 

Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	A	167	Homo sapiens	Mutation(s): 1  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Son of sevenless homolog 1	B	482	Homo sapiens	Mutation(s): 0  Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens) Explore Q07889  Go to UniProtKB:  Q07889
PHAROS:  Q07889

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase HRas	C	167	Homo sapiens	Mutation(s): 0  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
FFV	F [auth B]	N~2~-(3-chloro-4-fluorophenyl)-N~4~-[(1R)-1-cyclopropylethyl]quinazoline-2,4-diamine C19 H18 Cl F N4 LSMKBOZJAWCJNL-LLVKDONJSA-N
GOL	L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	G [auth B], H [auth B], I [auth B], J [auth B], K [auth B], N [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	O [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
FFV	BindingDB:  6CUP	EC50: 6400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.174 
• R-Value Work: 0.161 
• R-Value Observed: 0.161 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.654	α = 90
b = 184.654	β = 90
c = 179.351	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-26 
• Released Date: 2019-02-06 
Deposition Author(s): Phan, J., Abbott, J., Fesik, S.W.

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Funding Organization	Location	Grant Number
	United States	Lustgarten

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release