Research workbench
Crystal structure of human dual specificity protein kinase (ttk) in complex with a pyrimido-diazepin ligand
Analyse Crystal structure of human dual specificity protein kinase (ttk) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H9F
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- 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
- 92M, MG
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dual specificity protein kinase ttk (EC 2.7.12.1) | protein | 263 | 38% helix, 21% strand | P33981 |
Ligands and binding sites
- 92M · 9-cyclopentyl-2-(4-(4-hydroxypiperidin-1-yl)-2-methoxyphenylamino)-5-methyl-8,9-dihydro-5H-pyrimido[4,5-b][1,4]diazepin -6(7H)-one · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.75 | 0.87 | 46 | 92M |
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 3H9F · Crystal Structure of Human Dual Specificity Protein Kinase (TTK) in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P33981 · AlphaFold monomer V2.0 prediction for dual specificity protein kinase ttk (P33981) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 3H9F · PDBe 3H9F · UniProt P33981
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