Research workbench
Dgy-06-116, a novel and selective covalent inhibitor of src kinase
Analyse Dgy-06-116, a novel and selective covalent inhibitor of src kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E6E
- Type
- protein
- Length
- 2,124 residues
- Chains
- 8
- 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
- P12931
- Ligands
- HVY
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 266 | 40% helix, 17% strand | P12931 |
| G, H | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 264 | 39% helix, 16% strand | P12931 |
Ligands and binding sites
- HVY · N-(2-chloro-6-methylphenyl)-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-4-{[2-(propanoylamino) phenyl]amino}pyrimidine-5-carboxamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.78 | 0.81 | 93 | HVY |
| 2 | 703 | 0.77 | 0.82 | 74 | HVY |
| 3 | 1120 | 0.76 | 0.78 | 96 | HVY |
| 4 | 519 | 0.73 | 0.82 | 55 | HVY |
| 5 | 225 | 0.69 | 0.86 | 32 | HVY |
Interfaces
17 interfaces between chains.
- A–B · 518 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 503 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 500 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 474 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 446 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6E6E · DGY-06-116, a novel and selective covalent inhibitor of SRC kinase · 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 P12931
- Elsewhere: RCSB PDB 6E6E · PDBe 6E6E · UniProt P12931
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