5C5P | pdb_00005c5p

CRYSTAL STRUCTURE OF HUMAN TANKYRASE-2 IN COMPLEX WITH A PYRANOPYRIDONE INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Fragment-Based Drug Design of Novel Pyranopyridones as Cell Active and Orally Bioavailable Tankyrase Inhibitors.

de Vicente, J.Tivitmahaisoon, P.Berry, P.Bolin, D.R.Carvajal, D.He, W.Huang, K.S.Janson, C.Liang, L.Lukacs, C.Petersen, A.Qian, H.Yi, L.Zhuang, Y.Hermann, J.C.

(2015) ACS Med Chem Lett 6: 1019-1024

  • DOI: https://doi.org/10.1021/acsmedchemlett.5b00251
  • Primary Citation Related Structures: 
    5C5P, 5C5Q, 5C5R

  • PubMed Abstract: 

    Tankyrase activity has been linked to the regulation of intracellular axin levels, which have been shown to be crucial for the Wnt pathway. Deregulated Wnt signaling is important for the genesis of many diseases including cancer. We describe herein the discovery and development of a new series of tankyrase inhibitors. These pyranopyridones are highly active in various cell-based assays. A fragment/structure based optimization strategy led to a compound with good pharmacokinetic properties that is suitable for in vivo studies and further development.


  • Organizational Affiliation
    • Discovery Chemistry, Non-clinical Safety, Discovery Technologies, and Discovery Oncology, Small Molecule Research, Pharma Research & Early Development, Hoffmann-La Roche Inc. , pRED, 340 Kingsland Street, Nutley, New Jersey 07110, United States.

Macromolecule Content 

  • Total Structure Weight: 55.7 kDa 
  • Atom Count: 3,851 
  • Modeled Residue Count: 415 
  • Deposited Residue Count: 480 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2A,
C [auth B]
191Homo 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2B [auth C],
D
49Homo 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
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0E0

Query on 0E0



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
(3R)-3-(1-hydroxy-2-methylpropan-2-yl)-1,3,4,5-tetrahydro-6H-pyrano[4,3-c]isoquinolin-6-one
C16 H19 N O3
PZJOZWXZBQXTLD-CQSZACIVSA-N
SO4

Query on SO4



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

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.803α = 90
b = 98.471β = 90
c = 117.321γ = 90
Software Package:
Software NamePurpose
CNXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description