6M91

Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Prospective discovery of small molecule enhancers of an E3 ligase-substrate interaction.

Simonetta, K.R.Taygerly, J.Boyle, K.Basham, S.E.Padovani, C.Lou, Y.Cummins, T.J.Yung, S.L.von Soly, S.K.Kayser, F.Kuriyan, J.Rape, M.Cardozo, M.Gallop, M.A.Bence, N.F.Barsanti, P.A.Saha, A.

(2019) Nat Commun 10: 1402-1402

  • DOI: 10.1038/s41467-019-09358-9
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Protein-protein interactions (PPIs) governing the recognition of substrates by E3 ubiquitin ligases are critical to cellular function. There is significant therapeutic potential in the development of small molecules that modulate these interactions; ...

    Protein-protein interactions (PPIs) governing the recognition of substrates by E3 ubiquitin ligases are critical to cellular function. There is significant therapeutic potential in the development of small molecules that modulate these interactions; however, rational design of small molecule enhancers of PPIs remains elusive. Herein, we report the prospective identification and rational design of potent small molecules that enhance the interaction between an oncogenic transcription factor, β-Catenin, and its cognate E3 ligase, SCF β-TrCP . These enhancers potentiate the ubiquitylation of mutant β-Catenin by β-TrCP in vitro and induce the degradation of an engineered mutant β-Catenin in a cellular system. Distinct from PROTACs, these drug-like small molecules insert into a naturally occurring PPI interface, with contacts optimized for both the substrate and ligase within the same small molecule entity. The prospective discovery of 'molecular glue' presented here provides a paradigm for the development of small molecule degraders targeting hard-to-drug proteins.


    Organizational Affiliation

    5AM Ventures, 501 2nd Street, Suite 350, San Francisco, CA, 94107, USA. sahaanjanabha@gmail.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
F-box/WD repeat-containing protein 1A
A
432Homo sapiensMutation(s): 0 
Gene Names: BTRCBTRCPFBW1AFBXW1A
Find proteins for Q9Y297 (Homo sapiens)
Go to UniProtKB:  Q9Y297
NIH Common Fund Data Resources
PHAROS  Q9Y297

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S-phase kinase-associated protein 1
B
144Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
Find proteins for P63208 (Homo sapiens)
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS  P63208

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Catenin beta-1
C
33Homo sapiensMutation(s): 0 
Gene Names: CTNNB1CTNNBOK/SW-cl.35PRO2286
Find proteins for P35222 (Homo sapiens)
Go to UniProtKB:  P35222
NIH Common Fund Data Resources
PHAROS  P35222
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J97
Query on J97

Download CCD File 
A
3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid
C20 H11 Cl2 F3 N2 O4 S
HFBGFWJURBVNFD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
CL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.49α = 90
b = 82.49β = 90
c = 111.96γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references