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Crystal structure of human MYT1 kinase domain bounded with compound 39
Analyse Crystal structure of human MYT1 kinase domain bounded with compound 39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8D6D
- Type
- protein
- Length
- 544 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
- QGY, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% 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 | 270 | 38% helix, 20% strand | Q99640 |
| B | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 274 | 37% helix, 20% strand | Q99640 |
Ligands and binding sites
- QGY · (1P)-2-amino-5-bromo-1-(3-hydroxy-2,6-dimethylphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.72 | 0.82 | 54 | EDO, QGY |
| 2 | 392 | 0.69 | 0.81 | 46 | QGY |
| 3 | 120 | 0.47 | 0.79 | 18 | empty |
| 4 | 86 | 0.39 | 0.78 | 17 | empty |
| 5 | 75 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 310 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 8D6D · Crystal Structure of Human Myt1 Kinase domain Bounded with compound 39 · 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 B against A, TM-score 0.99
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 8D6D · PDBe 8D6D · UniProt Q99640
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