6CUP

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

    Department of Biochemistry and Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRas167Homo sapiensMutation(s): 1 
Gene Names: HRASHRAS1
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Son of sevenless homolog 1482Homo sapiensMutation(s): 0 
Gene Names: SOS1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
GTEx:  ENSG00000115904 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07889
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase HRas167Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
FFV
Query on FFV

Download Ideal Coordinates CCD File 
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
Query on GOL

Download Ideal Coordinates CCD File 
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
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
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Binding Affinity Annotations 
IDSourceBinding 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 = 184.654α = 90
b = 184.654β = 90
c = 179.351γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesLustgarten

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection