Research workbench
Crystal structure of human MYT1 kinase domain in complex with MK1775
Analyse Crystal structure of human MYT1 kinase domain in complex with MK1775 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VD0
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Homo sapiens
- Molecule
- Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
- EC
- 2.7.11.1
- UniProt
- Q99640
- Ligands
- 8X7
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.13 · 1 distinct chain · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase (EC 2.7.11.1) | protein | 293 | 38% helix, 18% strand | Q99640 |
Ligands and binding sites
- 8X7 · 1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one · ligand · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.70 | 0.79 | 62 | 8X7 |
| 2 | 60 | 0.31 | 0.76 | 15 | empty |
Compared structures
- 5VD0 · Crystal structure of human MYT1 kinase domain in complex with MK1775 · 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 0.97
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 5VD0 · PDBe 5VD0 · UniProt Q99640
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