Research workbench
Crystal structure of the C-abl kinase domain in complex with sti-571.
Analyse Crystal structure of the C-abl kinase domain in complex with sti-571. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IEP
- Type
- protein
- Length
- 548 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase abl
- EC
- 2.7.1.112
- UniProt
- P00520
- Ligands
- STI, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase abl (EC 2.7.1.112) | protein | 274 | 41% helix, 16% strand | P00520 |
Ligands and binding sites
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 6 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 524 | 0.75 | 0.83 | 52 | CL, STI |
| 2 | 634 | 0.75 | 0.81 | 62 | CL, STI |
| 3 | 69 | 0.46 | 0.82 | 20 | empty |
| 4 | 62 | 0.46 | 0.83 | 16 | empty |
| 5 | 89 | 0.40 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1IEP · Crystal structure of the C-abl kinase domain in complex with sti-571. · 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 B against A, TM-score 0.90
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 1IEP · PDBe 1IEP · UniProt P00520
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