6M90

Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 

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:  

  • 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

    Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,NiKang Therapeutics, Bldg. E500, 200 Powder Mill Road, Wilmington, DE, 19803, USA.,5AM Ventures, 501 2nd Street, Suite 350, San Francisco, CA, 94107, USA. sahaanjanabha@gmail.com.,Nurix Therapeutics, Inc., 1700 Owens Street, Suite 205, San Francisco, CA, 94158, USA. ksimonetta@nurix-inc.com.,BioArdis, 7310 Miramar Road San Diego, San Diego, CA, 92126, USA.,5AM Ventures, 501 2nd Street, Suite 350, San Francisco, CA, 94107, USA.,Nurix Therapeutics, Inc., 1700 Owens Street, Suite 205, San Francisco, CA, 94158, USA.,Nurix Therapeutics, Inc., 1700 Owens Street, Suite 205, San Francisco, CA, 94158, 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: BTRC (BTRCP, FBW1A, FBXW1A)
Find proteins for Q9Y297 (Homo sapiens)
Go to Gene View: BTRC
Go to UniProtKB:  Q9Y297
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Skp1
B
144Homo sapiensMutation(s): 0 
Gene Names: SKP1 (EMC19, OCP2, SKP1A, TCEB1L)
Find proteins for P63208 (Homo sapiens)
Go to Gene View: SKP1
Go to UniProtKB:  P63208
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Catenin beta-1
C
33Homo sapiensMutation(s): 0 
Gene Names: CTNNB1 (CTNNB)
Find proteins for P35222 (Homo sapiens)
Go to Gene View: CTNNB1
Go to UniProtKB:  P35222
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
J91
Query on J91

Download SDF File 
Download CCD File 
A
2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid
C20 H12 F4 N2 O5
KMUJGCDCPZZCCV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.178 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 82.760α = 90.00
b = 82.760β = 90.00
c = 111.820γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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