Research workbench
Crystal structure of CLK1 in complex with inhibitor 16
Analyse Crystal structure of CLK1 in complex with inhibitor 16 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FT9
- Type
- protein
- Length
- 1,010 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase CLK1
- EC
- 2.7.12.1
- UniProt
- P49759
- Ligands
- E6W, NA, BR, PO4
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 336 | 40% helix, 21% strand | P49759 |
| B, C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 40% helix, 21% strand | P49759 |
Ligands and binding sites
- E6W · 2-bromanyl-3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- BR · Bromide ion · ion · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.77 | 0.85 | 57 | PO4, GOL |
| 2 | 170 | 0.70 | 0.88 | 23 | E6W |
| 3 | 422 | 0.69 | 0.80 | 50 | E6W, BR |
| 4 | 178 | 0.68 | 0.86 | 24 | E6W, BR |
| 5 | 169 | 0.62 | 0.84 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 415 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 103 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6FT9 · Crystal structure of CLK1 in complex with inhibitor 16 · the same entry in another collection · chain A against A, TM-score 1.00
- P49759 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase CLK1 (P49759) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P49759
- Elsewhere: RCSB PDB 6FT9 · PDBe 6FT9 · UniProt P49759
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