TTBK1 in complex with inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


X-Ray Structural Analysis of Tau-Tubulin Kinase 1 and its Interactions with Small Molecular Inhibitors.

Xue, Y.Wan, P.T.Hillertz, P.Schweikart, F.Zhao, Y.Wissler, L.Dekker, N.

(2013) ChemMedChem 8: 1846

  • DOI: https://doi.org/10.1002/cmdc.201300274
  • Primary Citation of Related Structures:  
    4BTJ, 4BTK, 4BTM

  • PubMed Abstract: 

    Tau-tubulin kinase 1 (TTBK1) is a serine/threonine/tyrosine kinase that putatively phosphorylates residues including S422 in tau protein. Hyperphosphorylation of tau protein is the primary cause of tau pathology and neuronal death associated with Alzheimer's disease. A library of 12 truncation variants comprising the TTBK1 kinase domain was screened for expression in Escherichia coli and insect cells. One variant (residues 14-313) could be purified, but mass spectrometric analysis revealed extensive phosphorylation of the protein. Co-expression with lambda phosphatase in E. coli resulted in production of homogeneous, nonphosphorylated TTBK1. Binding of ATP and several compounds to TTBK1 was characterized by surface plasmon resonance. Crystal structures of TTBK1 in the unliganded form and in complex with ATP, and two high-affinity ATP-competitive inhibitors, 3-[(6,7-dimethoxyquinazolin-4-yl)amino]phenol (1) and methyl 2-bromo-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)benzoate (2), were elucidated. The structure revealed two clear basic patches near the ATP pocket providing an explanation of TTBK1 for phosphorylation-primed substrates. Interestingly, compound 2 displayed slow binding kinetics to TTBK1, the structure of TTBK1 in complex with this compound revealed a reorganization of the L199-D200 peptide backbone conformation together with altered hydrogen bonding with compound 2. These conformational changes necessary for the binding of compound 2 are likely the basis of the slow kinetics. This first TTBK1 structure can assist the discovery of novel inhibitors for the treatment of Alzheimer's disease.

  • Organizational Affiliation

    Discovery Sciences, AstraZeneca R&D Mölndal, 43183 Mölndal (Sweden). yafeng.xue@astrazeneca.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TAU-TUBULIN KINASE 1337Homo sapiensMutation(s): 0 
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TCY1 (Homo sapiens)
Explore Q5TCY1 
Go to UniProtKB:  Q5TCY1
GTEx:  ENSG00000146216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TCY1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DTQ

Download Ideal Coordinates CCD File 
C16 H15 N3 O3
Query on DMS

Download Ideal Coordinates CCD File 
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
DTQ PDBBind:  4BTK Kd: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.94α = 90
b = 40.28β = 104.24
c = 50.27γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-25
    Type: Initial release
  • Version 1.1: 2013-12-25
    Changes: Database references
  • Version 1.2: 2017-03-29
    Changes: Source and taxonomy
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other