Research workbench
Crystal structure of src kinase domain in complex with covalent inhibitor PD168393
Analyse Crystal structure of src kinase domain in complex with covalent inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HWP
- 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
- DJK
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 245 | 42% helix, 13% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 239 | 43% helix, 17% strand | P00523 |
Ligands and binding sites
- DJK · N-[4-(3-bromo-phenylamino)-quinazolin-6-yl]-acrylamide · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.59 | 0.78 | 38 | DJK |
| 2 | 313 | 0.55 | 0.76 | 30 | empty |
| 3 | 293 | 0.51 | 0.74 | 36 | DJK |
| 4 | 81 | 0.41 | 0.78 | 12 | empty |
| 5 | 61 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2HWP · Crystal structure of Src kinase domain in complex with covalent inhibitor PD168393 · 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 2HWP · PDBe 2HWP · UniProt P00523
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.