6BVM

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling.

Abbott, J.R., Hodges, T.R., Daniels, R.N., Patel, P.A., Kennedy, J.P., Howes, J.E., Akan, D.T., Burns, M.C., Sai, J., Sobolik, T., Beesetty, Y., Lee, T., Rossanese, O.W., Phan, J., Waterson, A.G., Fesik, S.W.

(2018) J Med Chem 61: 6002-6017

  • DOI: 10.1021/acs.jmedchem.8b00360
  • Primary Citation of Related Structures:  
    6BVI, 6BVK, 6BVJ, 6BVM, 6BVL

  • PubMed Abstract: 

    • Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS acti ...

    Deregulated RAS activity, often the result of mutation, is implicated in approximately 30% of all human cancers. Despite this statistic, no clinically successful treatment for RAS-driven tumors has yet been developed. One approach for modulating RAS activity is to target and affect the activity of proteins that interact with RAS, such as the guanine nucleotide exchange factor (GEF) son of sevenless homologue 1 (SOS1). Here, we report on structure-activity relationships (SAR) in an indole series of compounds. Using structure-based design, we systematically explored substitution patterns on the indole nucleus, the pendant amino acid moiety, and the linker unit that connects these two fragments. Best-in-class compounds activate the nucleotide exchange process at submicromolar concentrations in vitro, increase levels of active RAS-GTP in HeLa cells, and elicit signaling changes in the mitogen-activated protein kinase-extracellular regulated kinase (MAPK-ERK) pathway, resulting in a decrease in pERK1/2 T202/Y204 protein levels at higher compound concentrations.

    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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRas A167Homo sapiensMutation(s): 1 
Gene Names: HRAS, HRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
GTEx:  ENSG00000174775
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Son of sevenless homolog 1 B482Homo sapiensMutation(s): 0 
Gene Names: SOS1
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
NIH Common Fund Data Resources
PHAROS:  Q07889
GTEx:  ENSG00000115904
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRas C167Homo sapiensMutation(s): 0 
Gene Names: HRAS, HRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
GTEx:  ENSG00000174775
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
EBV
Query on EBV
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B
(2S)-2-amino-1-[(3aR,6aS)-5-[(5-chloro-1H-indol-3-yl)methyl]hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-3-(1H-indol-3-yl)propan-1-one
C26 H28 Cl N5 O
HTHTZBDFQBOXDD-YYDVJCTNSA-N		 Ligand Interaction
GOL
Query on GOL
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B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
FMT
Query on FMT
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B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO		AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.316α = 90
b = 184.316β = 90
c = 179.059γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Lustgarden FoundationUnited States--

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references