Research workbench
EGFR kinase domain mutant (T790M/L858R) with covalent ligand ns-062
Analyse EGFR kinase domain mutant (T790M/L858R) with covalent ligand ns-062 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y25
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- 8LU
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 36% helix, 18% strand | P00533 |
Ligands and binding sites
- 8LU · (2R)-N-[4-[(3-chloranyl-4-fluoranyl-phenyl)amino]-7-(3-morpholin-4-ylpropoxy)quinazolin-6-yl]-1-(2-fluoranylethanoyl)pyrrolidine-2-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.62 | 0.78 | 32 | 8LU |
| 2 | 144 | 0.52 | 0.80 | 23 | empty |
| 3 | 64 | 0.30 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Y25 · EGFR kinase domain mutant (T790M/L858R) with covalent ligand NS-062 · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00533
- Elsewhere: RCSB PDB 5Y25 · PDBe 5Y25 · UniProt P00533
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