7ZHQ

Crystal structure of TTBK1 in complex with compound 10 (7-009)

PDB DOI: https://doi.org/10.2210/pdb7ZHQ/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-04-06 Released: 2023-04-19
Deposition Author(s): Chaikuad, A., Axtman, A., Knapp, S., Structural Genomics Consortium (SGC)
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.212
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis.

Bashore, F.M., Marquez, A.B., Chaikuad, A., Howell, S., Dunn, A.S., Beltran, A.A., Smith, J.L., Drewry, D.H., Beltran, A.S., Axtman, A.D.

(2023) Sci Rep 13: 6118-6118

PubMed: 37059819 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-023-32854-4
Primary Citation of Related Structures:
7ZHN, 7ZHO, 7ZHP, 7ZHQ

PubMed Abstract:
Tau tubulin kinase 1 and 2 (TTBK1/2) are highly homologous kinases that are expressed and mediate disease-relevant pathways predominantly in the brain. Distinct roles for TTBK1 and TTBK2 have been delineated. While efforts have been devoted to characterizing the impact of TTBK1 inhibition in diseases like Alzheimer's disease and amyotrophic lateral sclerosis, TTBK2 inhibition has been less explored. TTBK2 serves a critical function during cilia assembly. Given the biological importance of these kinases, we designed a targeted library from which we identified several chemical tools that engage TTBK1 and TTBK2 in cells and inhibit their downstream signaling. Indolyl pyrimidinamine 10 significantly reduced the expression of primary cilia on the surface of human induced pluripotent stem cells (iPSCs). Furthermore, analog 10 phenocopies TTBK2 knockout in iPSCs, confirming a role for TTBK2 in ciliogenesis.

Organizational Affiliation

Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.

Macromolecule Content

Total Structure Weight: 36.52 kDa
Atom Count: 2,665
Modelled Residue Count: 293
Deposited Residue Count: 309
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tau-tubulin kinase 1	A	309	Homo sapiens	Mutation(s): 0 Gene Names: TTBK1, BDTK, KIAA1855 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5TCY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IRD (Subject of Investigation/LOI) Query on IRD Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	(3~{S})-1-(4-azanyl-3,5,12-triazatetracyclo[9.7.0.0^{2,7}.0^{13,18}]octadeca-1(11),2,4,6,13(18),14,16-heptaen-16-yl)-3-methyl-pent-1-yn-3-ol C₂₁ H₂₂ N₄ O ALQLTPNCVCECNJ-NRFANRHFSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]