MolNFT v1 · #137077 · protein
Crystal structure of human MYT1 kinase domain in complex with pha- 848125
5VD1 · Membrane-associated tyrosine- and threonine-specific CDC2…: “Crystal structure of human MYT1 kinase domain in complex with pha- 848125”. X-ray diffraction, 1 ligand (P48), 4 pockets (best druggability 0.69). MolNFT v1 #137077 on…
- PDB
- 5VD1
- Type
- protein
- Length
- 295 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
- P48
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 295 | 36% helix, 18% strand | Q99640 |
Ligands and binding sites
- P48 · N,1,4,4-tetramethyl-8-{[4-(4-methylpiperazin-1-yl) phenyl]amino}-4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline-3-carboxamide · 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.69 | 0.81 | 45 | P48 |
| 2 | 90 | 0.41 | 0.78 | 21 | empty |
| 3 | 120 | 0.39 | 0.75 | 19 | empty |
| 4 | 69 | 0.27 | 0.72 | 18 | empty |
Compared structures
- 5VD1 · Crystal structure of human MYT1 kinase domain in complex with pha-848125 · 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 5VD1 · PDBe 5VD1 · UniProt Q99640
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