Research workbench
Crystal structure of human MYT1 kinase domain in complex with pelitinib
Analyse Crystal structure of human MYT1 kinase domain in complex with pelitinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VCW
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase
- EC
- 2.7.11.1
- UniProt
- Q99640
- Ligands
- 93J, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 285 | 36% helix, 19% strand | Q99640 |
Ligands and binding sites
- 93J · (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-3-cyano-7-ethoxyquinolin-6-yl}-4-(dimethylamino)but-2-enamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.72 | 0.81 | 58 | 93J |
| 2 | 452 | 0.72 | 0.82 | 59 | 93J |
| 3 | 174 | 0.55 | 0.80 | 29 | empty |
| 4 | 95 | 0.40 | 0.77 | 20 | empty |
| 5 | 58 | 0.40 | 0.81 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 417 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VCW · CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH Pelitinib · the same entry in another collection · chain A against A, TM-score 1.00
- Q99640 · AlphaFold monomer V2.0 prediction for membrane-associated tyrosine- and… · 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 Q99640
- Elsewhere: RCSB PDB 5VCW · PDBe 5VCW · UniProt Q99640
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