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CLK3 bound with benzothiazole Tg003 (Cpd 2)

Analyse CLK3 bound with benzothiazole Tg003 (Cpd 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YTW
Type: protein
Length: 688 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Homo sapiens
Molecule: Dual specificity protein kinase CLK3
EC: 2.7.12.1
UniProt: P49761
Ligands: EAE, PO4, CL
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · resolution 2 · 2 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dual specificity protein kinase CLK3 (EC 2.7.12.1)	protein	349	40% helix, 19% strand	P49761
B	Dual specificity protein kinase CLK3 (EC 2.7.12.1)	protein	339	39% helix, 19% strand	P49761

Ligands and binding sites

EAE · (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one · ligand · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
GOL · Glycerol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	350	0.63	0.78	29	EDO, EAE
2	350	0.62	0.78	31	EAE
3	421	0.61	0.77	32	EDO
4	51	0.25	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 308 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6YTW · CLK3 bound with benzothiazole TG003 (cpd 2) · the same entry in another collection · chain A against A, TM-score 1.00
P49761 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK3 (P49761) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P49761
Elsewhere: RCSB PDB 6YTW · PDBe 6YTW · UniProt P49761

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