MolNFT v1 · #152036 · protein
Crystal structure of CLK1 in complexed with FURO[3,2-B]PYRIDINE compound VN345 (derivative of compound 12H)
6I5K · Dual specificity protein kinase CLK1: “Crystal structure of CLK1 in complexed with FURO[3,2-B]PYRIDINE compound VN345 (derivative of compound 12H)”. X-ray diffraction, 2 ligands (H3H, PO4), 11 pockets (best druggability 0.84).…
- PDB
- 6I5K
- Type
- protein
- Length
- 1,011 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
- H3H, PO4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 39% helix, 20% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 336 | 40% helix, 20% strand | P49759 |
| C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 338 | 39% helix, 20% strand | P49759 |
Ligands and binding sites
- H3H · 5-(1-methylpyrazol-4-yl)-3-(3-propan-2-yloxyphenyl) furo[3,2-b]pyridine · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · chains A, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.84 | 0.85 | 117 | GOL, H3H |
| 2 | 541 | 0.77 | 0.84 | 49 | GOL, H3H |
| 3 | 431 | 0.72 | 0.83 | 52 | GOL, H3H |
| 4 | 345 | 0.63 | 0.79 | 46 | empty |
| 5 | 87 | 0.43 | 0.79 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 852 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 189 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6I5K · Crystal structure of CLK1 in complexed with furo[3,2-b]pyridine compound VN345… · 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 6I5K · PDBe 6I5K · UniProt P49759
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