MolNFT v1 · #35133 · protein
Crystal structure of the C-abl kinase domain in complex with inno-406
2E2B · Proto-oncogene tyrosine-protein kinase ABL1: “Crystal structure of the C-abl kinase domain in complex with inno-406”. X-ray diffraction, 1 ligand (406), 4 pockets (best druggability 0.75). MolNFT v1 #35133 on GenesisL1: 3D…
- PDB
- 2E2B
- Type
- protein
- Length
- 532 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
- 406
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 270 | 44% helix, 16% strand | P00519 |
| B | Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) | protein | 262 | 42% helix, 16% strand | P00519 |
Ligands and binding sites
- 406 · N-[3-(4,5'-bipyrimidin-2-ylamino)-4-methylphenyl]-4-{[(3S)-3-(dimethylamino)pyrrolidin-1-yl]methyl}-3-(trifluoromethyl) benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.75 | 0.82 | 49 | 406 |
| 2 | 441 | 0.73 | 0.82 | 47 | 406 |
| 3 | 68 | 0.46 | 0.82 | 17 | empty |
| 4 | 61 | 0.45 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 541 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2E2B · Crystal structure of the c-Abl kinase domain in complex with INNO-406 · 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 0.92
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 2E2B · PDBe 2E2B · UniProt P00519
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