Research workbench
C-Src in complex with ibrutinib
Analyse C-Src in complex with ibrutinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L8L
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.888
- Source
- Gallus gallus
- Molecule
- Proto-oncogene tyrosine-protein kinase Src
- EC
- 2.7.10.2
- UniProt
- P00523
- Ligands
- 1E8
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.888 · 4 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) | protein | 258 | 34% helix, 15% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) | protein | 256 | 37% helix, 16% strand | P00523 |
| C | Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) | protein | 258 | 36% helix, 16% strand | P00523 |
| D | Proto-oncogene tyrosine-protein kinase Src (EC 2.7.10.2) | protein | 256 | 34% helix, 16% strand | P00523 |
Ligands and binding sites
- 1E8 · 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.79 | 0.82 | 80 | 1E8 |
| 2 | 1037 | 0.77 | 0.79 | 81 | 1E8 |
| 3 | 684 | 0.75 | 0.80 | 65 | 1E8 |
| 4 | 440 | 0.73 | 0.82 | 50 | 1E8 |
| 5 | 223 | 0.57 | 0.79 | 31 | empty |
Interfaces
4 interfaces between chains.
- C–D · 503 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 45 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6L8L · C-src in complex with ibrutinib · 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 6L8L · PDBe 6L8L · UniProt P00523
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.