Research workbench
X-ray crystal structure of dasatinib (bms-354825) bound to activated abl kinase domain
Analyse X-ray crystal structure of dasatinib (bms-354825) bound to activated abl kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GQG
- Type
- protein
- Length
- 555 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
- P00519
- Ligands
- 1N1
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 278 | 39% helix, 18% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 277 | 39% helix, 17% strand | P00519 |
Ligands and binding sites
- 1N1 · N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.68 | 0.82 | 42 | 1N1 |
| 2 | 356 | 0.68 | 0.81 | 43 | 1N1 |
| 3 | 65 | 0.50 | 0.85 | 15 | empty |
| 4 | 77 | 0.46 | 0.82 | 16 | empty |
| 5 | 84 | 0.38 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 547 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2GQG · X-ray Crystal Structure of Dasatinib (BMS-354825) Bound to Activated ABL Kinase Domain · 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 B against A, TM-score 0.93
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 2GQG · PDBe 2GQG · UniProt P00519
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