Research workbench
Crystal structure of ttk kinase domain with an inhibitor: 401498 (N- [(1R)-1-(2-CHLOROPHENYL)PROPYL]-3-{4-[(1-methylpiperidin-4-yl) OXY]PHENYL}-1H-indazole-5-carboxamide)
Analyse Crystal structure of ttk kinase domain with an inhibitor: 401498 (N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O6L
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dual specificity protein kinase ttk
- EC
- 2.7.12.1
- UniProt
- P33981
- Ligands
- 2QK
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase ttk (EC 2.7.12.1) | protein | 260 | 36% helix, 22% strand | P33981 |
| B | Dual specificity protein kinase ttk (EC 2.7.12.1) | protein | 256 | 37% helix, 21% strand | P33981 |
Ligands and binding sites
- 2QK · N-[(1R)-1-(2-chlorophenyl)propyl]-3-{4-[(1-methylpiperidin-4-yl)oxy]phenyl}-1H-indazole-5-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 528 | 0.77 | 0.84 | 56 | 2QK |
| 2 | 550 | 0.71 | 0.80 | 54 | 2QK |
| 3 | 61 | 0.33 | 0.77 | 14 | empty |
| 4 | 53 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 4O6L · Crystal Structure of TTK kinase domain with an inhibitor: 401498… · the same entry in another collection · chain A against A, TM-score 1.00
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 P33981
- Elsewhere: RCSB PDB 4O6L · PDBe 4O6L · UniProt P33981
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