4BTM

TTBK1 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 Alz ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TAU-TUBULIN KINASE 1A, B337Homo sapiensMutation(s): 0 
Gene Names: TTBK1BDTKKIAA1855
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
Find proteins for Q5TCY1 (Homo sapiens)
Explore Q5TCY1 
Go to UniProtKB:  Q5TCY1
NIH Common Fund Data Resources
PHAROS  Q5TCY1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8E
Query on F8E

Download CCD File 
A, B
methyl 2-bromo-5-(7H-pyrrolo[2,3-d]pyrimidin-4-ylamino)benzoate
C14 H11 Br N4 O2
YHDDNFHODNKNQV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F8EKd :  4100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.59α = 90
b = 108.42β = 94.14
c = 110.76γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: Derived calculations, Source and taxonomy