Research workbench
Drug resistant csrc kinase domain in complex with covalent inhibitor PD168393
Analyse Drug resistant csrc kinase domain in complex with covalent inhibitor PD168393 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LOK
- Type
- protein
- Length
- 490 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
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 248 | 39% helix, 16% strand | P00523 |
| B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 242 | 37% 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.65 | 0.76 | 67 | DJK |
| 2 | 503 | 0.64 | 0.77 | 46 | empty |
| 3 | 164 | 0.54 | 0.80 | 23 | DJK |
| 4 | 68 | 0.49 | 0.83 | 17 | empty |
| 5 | 113 | 0.35 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 356 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3LOK · Drug resistant cSrc 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 3LOK · PDBe 3LOK · UniProt P00523
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