7CE4 | pdb_00007ce4

Tankyrase2 catalytic domain in complex with K-476


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7CE4

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The dual pocket binding novel tankyrase inhibitor K-476 enhances the efficacy of immune checkpoint inhibitor by attracting CD8 + T cells to tumors.

Kinosada, H.Okada-Iwasaki, R.Kunieda, K.Suzuki-Imaizumi, M.Takahashi, Y.Miyagi, H.Suzuki, M.Motosawa, K.Watanabe, M.Mie, M.Ishii, T.Ishida, H.Saito, J.I.Nakai, R.

(2021) Am J Cancer Res 11: 264-276

  • Primary Citation Related Structures: 
    7CE4

  • PubMed Abstract: 

    The Wnt/β-catenin pathway, which is associated with disease progression, is activated in many cancers. Tankyrase (TNKS) has received attention as a target molecule for Wnt/β-catenin pathway inhibition. We identified K-476, a novel TNKS inhibitor, a dual pocket binder that binds to both the nicotinamide and ADP-ribose pockets. In a human colon cancer cell line, K-476 specifically and potently inhibited TNKS and led to stabilization of the Axin protein, resulting in Wnt/β-catenin pathway suppression. Aberrant Wnt/β-catenin pathway activation was recently reported as a possible mechanism of ineffectiveness in immune checkpoint inhibitor (ICI) treatment. Because the Wnt/β-catenin pathway activation causes dendritic cell inactivation and suppresses chemokine production, resulting in a paucity of CD8 + T cells in tumor tissue, which is an important effector of ICIs. Thus, TNKS inhibitors may enhance the efficacy of ICIs. To examine whether K-476 enhances the antitumor effect of anti-PD-L1 antibodies, K-476 was administered orally with an anti-PD-L1 antibody to melanoma-bearing C57BL/6J mice. Although K-476 was ineffective as a monotherapy, it significantly enhanced the antitumor effect in combination with anti-PD-L1 antibody. In mice, intra-tumor infiltration of CD8 + T cells was increased by combination treatment. K-476 upregulated the chemokine expression (e.g., Ccl3 and Ccl4 ), which attracted CD8 + T cells. This was considered to contribute to the increased CD8 + T cells in the tumor microenvironment. Furthermore, while the potential gastrointestinal toxicity of TNKS inhibitors has been reported, it was not observed at effective doses. Thus, K-476 could be an attractive therapeutic option to enhance the efficacy of ICIs.


  • Organizational Affiliation
    • R&D Division, Kyowa Kirin Co., Ltd. Japan.

Macromolecule Content 

  • Total Structure Weight: 28.32 kDa 
  • Atom Count: 2,055 
  • Modeled Residue Count: 207 
  • Deposited Residue Count: 240 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase tankyrase-2191Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase tankyrase-249Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KK6
(Subject of Investigation/LOI)

Query on KK6



Download:Ideal Coordinates CCD File
F [auth A]5-[3-[[1-(6,7-dimethoxyquinazolin-4-yl)piperidin-4-yl]methyl]-2-oxidanylidene-4H-quinazolin-1-yl]-2-fluoranyl-benzenecarbonitrile
C31 H29 F N6 O3
STWRRCLLHUNQOS-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.203 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.534α = 90
b = 66.534β = 90
c = 116.815γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description