MolNFT v1 · #171115 · protein
CLK3 bound with benzothiazole TG003 (cpd 2)
6YTW · Dual specificity protein kinase CLK3: “CLK3 bound with benzothiazole TG003 (cpd 2)”. X-ray diffraction, 3 ligands (EAE, PO4, CL), 4 pockets (best druggability 0.63). MolNFT v1 #171115 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YTW
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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.
| Volume (ų) | 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 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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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