Research workbench
Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase mer in complex with inhibitor UNC1917
Analyse Crystal structure of the catalytic domain of the proto-oncogene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M3Q
- Type
- protein
- Length
- 479 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
- 24K, MG, CL
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 243 | 38% helix, 20% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 236 | 43% helix, 16% strand | Q12866 |
Ligands and binding sites
- 24K · trans-4-{[2-(butylamino)-5-(pyridin-2-yl)pyrimidin-4-yl]amino}cyclohexanol · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.66 | 0.78 | 45 | CL, MG, 24K |
| 2 | 487 | 0.65 | 0.77 | 50 | CL, 24K |
| 3 | 194 | 0.56 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1047 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4M3Q · Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase… · 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 A against A, TM-score 0.98
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 4M3Q · PDBe 4M3Q · UniProt Q12866
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