Research workbench
Crystal structure of an SH2-kinase domain construct of C-abl tyrosine kinase
Analyse Crystal structure of an SH2-kinase domain construct of C-abl tyrosine kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XEY
- Type
- protein
- Length
- 628 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
- 1N1
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 359 | 35% helix, 22% strand | P00519 |
| A | Tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 269 | 42% helix, 19% 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 B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.78 | 0.83 | 57 | empty |
| 2 | 412 | 0.65 | 0.78 | 43 | 1N1 |
| 3 | 198 | 0.62 | 0.82 | 20 | 1N1 |
| 4 | 92 | 0.49 | 0.81 | 21 | empty |
| 5 | 85 | 0.48 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- B–A · 699 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4XEY · Crystal structure of an SH2-kinase domain construct of c-Abl tyrosine kinase · the same entry in another collection · chain B against B, 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 4XEY · PDBe 4XEY · UniProt P00519
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