7QHW

TTBK1 kinase domain in complex with inhibitor 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

TDP-43 Modulation by Tau-Tubulin Kinase 1 Inhibitors: A New Avenue for Future Amyotrophic Lateral Sclerosis Therapy.

Nozal, V.Martinez-Gonzalez, L.Gomez-Almeria, M.Gonzalo-Consuegra, C.Santana, P.Chaikuad, A.Perez-Cuevas, E.Knapp, S.Lietha, D.Ramirez, D.Petralla, S.Monti, B.Gil, C.Martin-Requero, A.Palomo, V.de Lago, E.Martinez, A.

(2022) J Med Chem 65: 1585-1607

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01942
  • Primary Citation of Related Structures:  
    7Q8V, 7Q8W, 7Q8Y, 7Q8Z, 7Q90, 7QHW

  • PubMed Abstract: 

    Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease without any effective treatment. Protein TDP-43 is a pathological hallmark of ALS in both sporadic and familiar patients. Post-translational modifications of TDP-43 promote its aggregation in the cytoplasm. Tau-Tubulin kinase (TTBK1) phosphorylates TDP-43 in cellular and animal models; thus, TTBK1 inhibitors emerge as a promising therapeutic strategy for ALS. The design, synthesis, biological evaluation, kinase-ligand complex structure determination, and molecular modeling studies confirmed novel pyrrolopyrimidine derivatives as valuable inhibitors for further development. Moreover, compound 29 revealed good brain penetration in vivo and was able to reduce TDP-43 phosphorylation not only in cell cultures but also in the spinal cord of transgenic TDP-43 mice. A shift to M2 anti-inflammatory microglia was also demonstrated in vivo . Both these activities led to motor neuron preservation in mice, proposing pyrrolopyrimidine 29 as a valuable lead compound for future ALS therapy.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas─CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tau-tubulin kinase 1A [auth AAA],
B [auth CCC]
293Homo sapiensMutation(s): 0 
Gene Names: TTBK1BDTKKIAA1855
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TCY1 (Homo sapiens)
Explore Q5TCY1 
Go to UniProtKB:  Q5TCY1
PHAROS:  Q5TCY1
GTEx:  ENSG00000146216 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TCY1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CGI (Subject of Investigation/LOI)
Query on CGI

Download Ideal Coordinates CCD File 
C [auth AAA],
H [auth CCC]
~{N}-[4-(4-chloranylphenoxy)phenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
C18 H13 Cl N4 O
RWRSKMSFZCQDMQ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth AAA],
I [auth CCC],
J [auth CCC],
K [auth CCC]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA],
G [auth AAA]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CGI BindingDB:  7QHW IC50: 240 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.12α = 90
b = 108.463β = 94.512
c = 110.314γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Economy and Competitiveness (MINECO)SpainRTI2018-0988885-B-I00
Ministry of Economy and Competitiveness (MINECO)SpainRTI2018-099318-B-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description