5J1W

Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW31 (compound 14)

PDB DOI: https://doi.org/10.2210/pdb5J1W/pdb

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

Deposited: 2016-03-29 Released: 2016-05-04
Deposition Author(s): Chaikuad, A., Esvan, Y.J., Zeinyeh, W., Boibessot, T., Nauton, L., Thery, V., Loaec, N., Meijer, L., Giraud, F., Moreau, P., Anizon, F., von Delft, F., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.228
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of pyrido[3,4-g]quinazoline derivatives as CMGC family protein kinase inhibitors: Design, synthesis, inhibitory potency and X-ray co-crystal structure.

Esvan, Y.J., Zeinyeh, W., Boibessot, T., Nauton, L., Thery, V., Knapp, S., Chaikuad, A., Loaec, N., Meijer, L., Anizon, F., Giraud, F., Moreau, P.

(2016) Eur J Med Chem 118: 170-177

PubMed: 27128181 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2016.04.004
Primary Citation of Related Structures:
5J1V, 5J1W

PubMed Abstract:
The design and synthesis of new pyrido[3,4-g]quinazoline derivatives is described as well as their protein kinase inhibitory potencies toward five CMGC family members (CDK5, CK1, GSK3, CLK1 and DYRK1A). The interest for this original tricyclic heteroaromatic scaffold as modulators of CLK1/DYRK1A activity was validated by nanomolar potencies (compounds 12 and 13). CLK1 co-crystal structures with two inhibitors revealed the binding mode of these compounds within the ATP-binding pocket.

Organizational Affiliation

Université Clermont Auvergne, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France; CNRS, UMR 6296, ICCF, F-63178 Aubière, France.

Macromolecule Content

Total Structure Weight: 120.55 kDa
Atom Count: 8,253
Modelled Residue Count: 991
Deposited Residue Count: 1,017
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A, B, C	339	Homo sapiens	Mutation(s): 0 Gene Names: CLK1, CLK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens) Explore P49759 Go to UniProtKB: P49759
PHAROS: P49759 GTEx: ENSG00000013441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6FB Query on 6FB Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C]	I [auth A], L [auth B], Q [auth C], R [auth C]	pyrido[3,4-g]quinazolin-2-amine C₁₁ H₈ N₄ HTMYPIWEXZOFDM-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C]	K [auth B], P [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain K [auth B] Focus chain P [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File 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 J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] 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 J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], M [auth C], N [auth C], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions 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 J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density 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 J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]