5BXU | pdb_00005bxu

Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n4m5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.186 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5BXU

Ligand Structure Quality Assessment 


This is version 3.2 of the entry. See complete history

Literature

Macrocyclized Extended Peptides: Inhibiting the Substrate-Recognition Domain of Tankyrase.

Xu, W.Lau, Y.H.Fischer, G.Tan, Y.S.Chattopadhyay, A.de la Roche, M.Hyvonen, M.Verma, C.Spring, D.R.Itzhaki, L.S.

(2017) J Am Chem Soc 139: 2245-2256

  • DOI: https://doi.org/10.1021/jacs.6b10234
  • Primary Citation Related Structures: 
    5BXO, 5BXU

  • PubMed Abstract: 

    We report a double-click macrocyclization approach for the design of constrained peptide inhibitors having non-helical or extended conformations. Our targets are the tankyrase proteins (TNKS), poly(ADP-ribose) polymerases (PARP) that regulate Wnt signaling by targeting Axin for degradation. TNKS are deregulated in many different cancer types, and inhibition of TNKS therefore represents an attractive therapeutic strategy. However, clinical development of TNKS-specific PARP catalytic inhibitors is challenging due to off-target effects and cellular toxicity. We instead targeted the substrate-recognition domain of TNKS, as it is unique among PARP family members. We employed a two-component strategy, allowing peptide and linker to be separately engineered and then assembled in a combinatorial fashion via click chemistry. Using the consensus substrate-peptide sequence as a starting point, we optimized the length and rigidity of the linker and its position along the peptide. Optimization was further guided by high-resolution crystal structures of two of the macrocyclized peptides in complex with TNKS. This approach led to macrocyclized peptides with submicromolar affinities for TNKS and high proteolytic stability that are able to disrupt the interaction between TNKS and Axin substrate and to inhibit Wnt signaling in a dose-dependent manner. The peptides therefore represent a promising starting point for a new class of substrate-competitive inhibitors of TNKS with potential for suppressing Wnt signaling in cancer. Moreover, by demonstrating the application of the double-click macrocyclization approach to non-helical, extended, or irregularly structured peptides, we greatly extend its potential and scope, especially given the frequency with which such motifs mediate protein-protein interactions.


  • Organizational Affiliation
    • Department of Pharmacology, University of Cambridge , Tennis Court Road, Cambridge CB2 1PD, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 18.89 kDa 
  • Atom Count: 1,576 
  • Modeled Residue Count: 172 
  • Deposited Residue Count: 173 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2164Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens)
Explore Q9H2K2 
Go to UniProtKB:  Q9H2K2
PHAROS:  Q9H2K2
GTEx:  ENSG00000107854 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2K2
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
cp4n4m59Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4XQ

Query on 4XQ



Download:Ideal Coordinates CCD File
D [auth B]4,4'-pentane-1,5-diylbis(1-propyl-1H-1,2,3-triazole)
C15 H26 N6
MUTHZRDXMHMSAA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GMA
Query on GMA
B
L-PEPTIDE LINKINGC5 H10 N2 O3GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.086α = 90
b = 63.279β = 90
c = 72.325γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
Cootmodel building
REFMACrefinement
PHASERphasing
autoPROCdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1002329

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations
  • Version 3.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Refinement description
  • Version 3.1: 2024-02-07
    Changes: Refinement description
  • Version 3.2: 2026-05-13
    Changes: Database references, Structure summary