MolNFT v1 · #135684 · protein
Crystal structure of the mer kinase domain in complex with a macrocyclic inhibitor
5U6C · Tyrosine-protein kinase mer: “Crystal structure of the mer kinase domain in complex with a macrocyclic inhibitor”. X-ray diffraction, 1 ligand (7YS), 6 pockets (best druggability 0.70). MolNFT v1 #135684 on GenesisL1: 3D structure…
- PDB
- 5U6C
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase mer
- EC
- 2.7.10.1
- UniProt
- Q12866
- Ligands
- 7YS
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 272 | 41% helix, 17% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 257 | 42% helix, 19% strand | Q12866 |
Ligands and binding sites
- 7YS · (10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3, 10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno) pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.70 | 0.77 | 80 | 7YS |
| 2 | 205 | 0.60 | 0.81 | 21 | empty |
| 3 | 264 | 0.56 | 0.77 | 22 | 7YS |
| 4 | 122 | 0.54 | 0.81 | 14 | empty |
| 5 | 68 | 0.33 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1035 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5U6C · Crystal structure of the Mer kinase domain in complex with a macrocyclic inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q12866 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase mer (Q12866) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q12866
- Elsewhere: RCSB PDB 5U6C · PDBe 5U6C · UniProt Q12866
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