MolNFT v1 · #17314 · protein
Structural basis for the auto-inhibition of C-abl tyrosine kinase
1OPL · Proto-oncogene tyrosine-protein kinase: “Structural basis for the auto-inhibition of C-abl tyrosine kinase”. X-ray diffraction, 2 ligands (P16, MYR), 12 pockets (best druggability 0.76). MolNFT v1 #17314 on GenesisL1: 3D structure…
- PDB
- 1OPL
- Type
- protein
- Length
- 816 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase
- EC
- 2.7.1.112
- UniProt
- P00519
- Ligands
- P16, MYR
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase (EC 2.7.1.112) | protein | 451 | 31% helix, 23% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase (EC 2.7.1.112) | protein | 365 | 36% helix, 21% strand | P00519 |
Ligands and binding sites
- P16 · 6-(2,6-dichlorophenyl)-2-{[3-(hydroxymethyl)phenyl]amino}-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one · ligand · 2 copies · chains A, B
- MYR · Myristic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.76 | 0.78 | 63 | empty |
| 2 | 569 | 0.73 | 0.80 | 54 | P16 |
| 3 | 193 | 0.72 | 0.89 | 28 | P16 |
| 4 | 126 | 0.58 | 0.84 | 24 | MYR |
| 5 | 102 | 0.51 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 531 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1OPL · Structural basis for the auto-inhibition of c-Abl tyrosine kinase · the same entry in another collection · chain A against A, TM-score 1.00
- P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain A 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 P00519
- Elsewhere: RCSB PDB 1OPL · PDBe 1OPL · UniProt P00519
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