Research workbench
Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase mer in complex with inhibitor UNC2541
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
- 5K0X
- Type
- protein
- Length
- 512 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
- K0X, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 258 | 38% helix, 17% strand | Q12866 |
| B | Tyrosine-protein kinase mer (EC 2.7.10.1) | protein | 254 | 41% helix, 19% strand | Q12866 |
Ligands and binding sites
- K0X · (7S)-7-amino-N-[(4-fluorophenyl)methyl]-8-oxo-2,9,16, 18,21-pentaazabicyclo[15.3.1]henicosa-1(21),17,19-triene-20-carboxamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 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 | 546 | 0.73 | 0.81 | 68 | CL, K0X |
| 2 | 398 | 0.70 | 0.81 | 37 | K0X |
| 3 | 201 | 0.57 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1019 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5K0X · 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 B against A, TM-score 0.96
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 5K0X · PDBe 5K0X · UniProt Q12866
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