Research workbench
Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE derivative ZW31 (compound 14)
Analyse Crystal structure of human CLK1 in complex with PYRIDO[3,4- G]QUINAZOLINE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J1W
- Type
- protein
- Length
- 991 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
- 6FB, PO4
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 20% 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 | 316 | 39% helix, 21% strand | P49759 |
Ligands and binding sites
- 6FB · pyrido[3,4-g]quinazolin-2-amine · ligand · 4 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains B, C, A
- GOL · Glycerol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.75 | 0.78 | 88 | PO4, 6FB |
| 2 | 492 | 0.73 | 0.82 | 43 | GOL, 6FB |
| 3 | 644 | 0.70 | 0.77 | 61 | GOL, 6FB, PO4 |
| 4 | 425 | 0.68 | 0.80 | 47 | GOL, 6FB |
| 5 | 453 | 0.63 | 0.76 | 49 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 462 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 456 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J1W · Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW31… · 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 0.99
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 5J1W · PDBe 5J1W · UniProt P49759
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