MolNFT v1 · #191328 · protein
Crystal structure of human MYT1 kinase domain bounded with eph receptor inhibitor / compound 41
8D6F · Membrane-associated tyrosine- and threonine-specific CDC2…: “Crystal structure of human MYT1 kinase domain bounded with eph receptor inhibitor / compound 41”. X-ray diffraction, 2 ligands (QG5, SO4), 8 pockets (best druggability…
- PDB
- 8D6F
- Type
- protein
- Length
- 542 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
- QG5, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 272 | 39% helix, 19% strand | Q99640 |
| A | Membrane-associated tyrosine- and threonine-specific CDC2- inhibitory kinase (EC 2.7.11.1) | protein | 270 | 39% helix, 20% strand | Q99640 |
Ligands and binding sites
- QG5 · (1M)-2-amino-1-(5-hydroxy-2-methylphenyl)-1H-pyrrolo[2, 3-b]quinoxaline-3-carboxamide · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.74 | 0.81 | 74 | QG5 |
| 2 | 393 | 0.71 | 0.82 | 40 | QG5 |
| 3 | 126 | 0.47 | 0.78 | 27 | empty |
| 4 | 56 | 0.41 | 0.82 | 16 | empty |
| 5 | 83 | 0.36 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 377 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8D6F · Crystal Structure of Human Myt1 Kinase domain Bounded with Eph receptor inhibitor /… · the same entry in another collection · chain B against B, 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 8D6F · PDBe 8D6F · UniProt Q99640
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