Research workbench
Crystal structure of CLK1 in complex with compound 2 (CC513)
Analyse Crystal structure of CLK1 in complex with compound 2 (CC513) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OPG
- 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
- 06N, PO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 337 | 39% helix, 21% strand | P49759 |
| B | Dual specificity protein kinase CLK1 (EC 2.7.12.1) | protein | 338 | 39% helix, 21% strand | P49759 |
Ligands and binding sites
- 06N · 4-[2-(propylamino)imidazo[2,1-b][1,3,4]thiadiazol-5-yl]phenol · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 2 copies · chains B, C
- GOL · Glycerol · additive · 10 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.80 | 0.81 | 88 | GOL, 06N |
| 2 | 1101 | 0.74 | 0.77 | 72 | empty |
| 3 | 447 | 0.72 | 0.82 | 48 | 06N, GOL |
| 4 | 421 | 0.69 | 0.81 | 45 | 06N, GOL |
| 5 | 491 | 0.68 | 0.79 | 55 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 991 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 180 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7OPG · Crystal structure of CLK1 in complex with compound 2 (CC513) · the same entry in another collection · chain B against B, 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 7OPG · PDBe 7OPG · UniProt P49759
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