Research workbench
Strategic design of catalytic lysine-targeting reversible covalent BCR-abl inhibitors
Analyse Strategic design of catalytic lysine-targeting reversible covalent BCR-abl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DT2
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase ABL1
- EC
- 2.7.10.2
- UniProt
- P00519
- Ligands
- HJ9
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 265 | 43% helix, 17% strand | P00519 |
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 267 | 43% helix, 18% strand | P00519 |
Ligands and binding sites
- HJ9 · [4-[5-[5-(dimethylcarbamoyl)pyridin-3-yl]-1H-pyrrolo[2, 3-b]pyridin-3-yl]-2-methanoyl-5-methoxy-phenyl]boronic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.74 | 0.81 | 74 | HJ9 |
| 2 | 329 | 0.64 | 0.79 | 47 | HJ9 |
| 3 | 65 | 0.49 | 0.84 | 17 | empty |
| 4 | 82 | 0.46 | 0.81 | 18 | empty |
| 5 | 157 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 660 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7DT2 · Strategic design of catalytic lysine-targeting reversible covalent BCR-ABL Inhibitors · 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 0.96
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 P00519
- Elsewhere: RCSB PDB 7DT2 · PDBe 7DT2 · UniProt P00519
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