Research workbench
Targeted polypharmacology: crystal structure of the C-src kinase domain in complex with S1, a multitargeted kinase inhibitor
Analyse Targeted polypharmacology: crystal structure of the C-src kinase domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EN7
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- ABJ
- Pockets
- 4 · best druggability 0.69
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 src (EC 2.7.10.2) | protein | 247 | 44% helix, 15% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 237 | 42% helix, 17% strand | P00523 |
Ligands and binding sites
- ABJ · 3-[4-amino-1-(1-methylethyl)-1H-pyrazolo[3,4-d]pyrimidin-3-yl]phenol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.69 | 0.77 | 89 | ABJ |
| 2 | 407 | 0.62 | 0.77 | 45 | empty |
| 3 | 203 | 0.51 | 0.76 | 32 | empty |
| 4 | 55 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 371 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3EN7 · Targeted polypharmacology: crystal structure of the c-Src kinase domain in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 P00523
- Elsewhere: RCSB PDB 3EN7 · PDBe 3EN7 · UniProt P00523
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