Research workbench
Crystal structure of human MYT1 kinase domain (de-phosphorylated) in complex with saracatinib
Analyse Crystal structure of human MYT1 kinase domain (de-phosphorylated) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VD3
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- 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
- H8H
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% 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 | 37% helix, 17% strand | Q99640 |
Ligands and binding sites
- H8H · N-(5-chloro-1,3-benzodioxol-4-yl)-7-[2-(4-methylpiperazin-1-yl)ethoxy]-5-(tetrahydro-2H-pyran-4-yloxy)quinazolin-4-amine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 420 | 0.68 | 0.80 | 40 | H8H, EDO |
| 2 | 176 | 0.45 | 0.75 | 21 | empty |
Compared structures
- 5VD3 · CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (de-phosphorylated) IN COMPLEX WITH… · 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 5VD3 · PDBe 5VD3 · UniProt Q99640
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