Research workbench
Crystal structure of CLK1 in complexed with FURO[3,2-B]PYRIDINE compound VN316 (derivative of compound 12H)
Analyse Crystal structure of CLK1 in complexed with FURO[3,2-B]PYRIDINE compound VN316… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I5L
- Type
- protein
- Length
- 1,012 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
- H3Q, PO4
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 338 | 38% helix, 20% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 336 | 40% helix, 21% strand | P49759 |
Ligands and binding sites
- H3Q · 3-(3-cyclobutylphenyl)-5-(1-methylpyrazol-4-yl)furo[3, 2-b]pyridine · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 4 copies · chains A, C, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.84 | 0.85 | 123 | PO4, H3Q, GOL |
| 2 | 555 | 0.78 | 0.84 | 50 | H3Q, GOL |
| 3 | 450 | 0.73 | 0.82 | 51 | H3Q, GOL |
| 4 | 288 | 0.61 | 0.79 | 42 | empty |
| 5 | 85 | 0.43 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 883 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 181 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6I5L · Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN316… · 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 C 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 6I5L · PDBe 6I5L · UniProt P49759
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