6M94

Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

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
  • Primary Citation of Related Structures:  
    6M93, 6M92, 6M94, 6M91, 6M90

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
F-box/WD repeat-containing protein 1AA432Homo sapiensMutation(s): 0 
Gene Names: BTRCBTRCPFBW1AFBXW1A
Find proteins for Q9Y297 (Homo sapiens)
Explore Q9Y297 
Go to UniProtKB:  Q9Y297
NIH Common Fund Data Resources
PHAROS  Q9Y297
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S-phase kinase-associated protein 1B144Homo sapiensMutation(s): 0 
Gene Names: SKP1EMC19OCP2SKP1ATCEB1L
Find proteins for P63208 (Homo sapiens)
Explore P63208 
Go to UniProtKB:  P63208
NIH Common Fund Data Resources
PHAROS  P63208
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Catenin beta-1C33Homo sapiensMutation(s): 0 
Gene Names: CTNNB1CTNNBOK/SW-cl.35PRO2286
Find proteins for P35222 (Homo sapiens)
Explore P35222 
Go to UniProtKB:  P35222
NIH Common Fund Data Resources
PHAROS  P35222
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 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: 2.70 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.37α = 90
b = 82.37β = 90
c = 112.89γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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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