Crystal structure of SHANK1 PDZ in complex with a peptide-small molecule hybrid

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Identification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.

Hegedus, Z.Hobor, F.Shoemark, D.K.Celis, S.Lian, L.Y.Trinh, C.H.Sessions, R.B.Edwards, T.A.Wilson, A.J.

(2021) Chem Sci 12: 2286-2293

  • DOI: https://doi.org/10.1039/d0sc05694d
  • Primary Citation of Related Structures:  
    6YWZ, 6YX0, 6YX1, 6YX2

  • PubMed Abstract: 

    β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

  • Organizational Affiliation

    School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK a.j.wilson@leeds.ac.uk.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SH3 and multiple ankyrin repeat domains protein 1A [auth B],
B [auth A]
112Homo sapiensMutation(s): 0 
Gene Names: SHANK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y566 (Homo sapiens)
Explore Q9Y566 
Go to UniProtKB:  Q9Y566
GTEx:  ENSG00000161681 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y566
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PWN

Download Ideal Coordinates CCD File 
D [auth B],
H [auth A]
2-[(~{E})-(4-oxidanylidenebutanoylhydrazinylidene)methyl]benzoic acid
C12 H12 N2 O4
Query on ARG

Download Ideal Coordinates CCD File 
F [auth B],
J [auth A]
C6 H15 N4 O2
Query on LEU

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G [auth B],
K [auth A]
C6 H13 N O2
Query on THR

Download Ideal Coordinates CCD File 
E [auth B],
I [auth A]
C4 H9 N O3
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.566α = 90
b = 65.973β = 90
c = 86.904γ = 90
Software Package:
Software NamePurpose
DIALSdata processing
Aimlessdata scaling
pointlessdata scaling
Cootmodel building
DIALSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/N035267/1
European CommissionUnited KingdomMSCA-IF-2016-749012
Royal SocietyUnited KingdomSRF/R1/191087

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-07-07
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description