MolNFT v1 · #122851 · protein
Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE derivative ZW29 (compound 13)
5J1V · Dual specificity protein kinase CLK1: “Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE derivative ZW29 (compound 13)”. X-ray diffraction, 1 ligand (6FD), 10 pockets (best druggability 0.77). MolNFT v1…
- PDB
- 5J1V
- Type
- protein
- Length
- 989 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
- 6FD
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 338 | 40% helix, 20% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 40% helix, 20% strand | P49759 |
| C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 314 | 38% helix, 21% strand | P49759 |
Ligands and binding sites
- 6FD · pyrido[3,4-g]quinazoline-2,10-diamine · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 807 | 0.77 | 0.81 | 78 | empty |
| 2 | 614 | 0.71 | 0.79 | 54 | 6FD |
| 3 | 452 | 0.70 | 0.80 | 47 | 6FD |
| 4 | 213 | 0.67 | 0.85 | 25 | 6FD |
| 5 | 168 | 0.49 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 391 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 307 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 119 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5J1V · Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW29… · 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 B 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 5J1V · PDBe 5J1V · UniProt P49759
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