Research workbench
AP24534, a pan-BCR-abl inhibitor for chronic myeloid leukemia, potently inhibits the T315I mutant and overcomes mutation-based resistance
Analyse AP24534, a pan-BCR-abl inhibitor for chronic myeloid leukemia, potently… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IK3
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00520
- Ligands
- 0LI
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 280 | 46% helix, 16% strand | P00520 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 286 | 46% helix, 16% strand | P00520 |
Ligands and binding sites
- 0LI · 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl) phenyl}benzamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 767 | 0.77 | 0.81 | 65 | 0LI |
| 2 | 797 | 0.75 | 0.79 | 76 | 0LI |
| 3 | 350 | 0.52 | 0.73 | 43 | empty |
| 4 | 59 | 0.49 | 0.85 | 13 | empty |
| 5 | 74 | 0.46 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 395 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3IK3 · AP24534, a Pan-BCR-ABL Inhibitor for Chronic Myeloid Leukemia, Potently Inhibits the… · the same entry in another collection · chain A against A, TM-score 1.00
- P00520 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00520) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P00520
- Elsewhere: RCSB PDB 3IK3 · PDBe 3IK3 · UniProt P00520
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