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Crystal structure of mutant abl kinase domain in complex with small molecule fragment
Analyse Crystal structure of mutant abl kinase domain in complex with small molecule… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DK3
- Type
- protein
- Length
- 535 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
- SX7, SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 266 | 44% helix, 17% strand | P00520 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 269 | 42% helix, 17% strand | P00520 |
Ligands and binding sites
- SX7 · 2-amino-5-[3-(1-ethyl-1H-pyrazol-5-yl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylbenzamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains 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 | 293 | 0.64 | 0.80 | 38 | SX7 |
| 2 | 306 | 0.61 | 0.79 | 44 | SX7 |
| 3 | 78 | 0.48 | 0.82 | 19 | empty |
| 4 | 69 | 0.48 | 0.83 | 16 | empty |
| 5 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3DK3 · Crystal structure of mutant ABL kinase domain in complex with small molecule fragment · 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 0.96
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 P00520
- Elsewhere: RCSB PDB 3DK3 · PDBe 3DK3 · UniProt P00520
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