Research workbench
EGFR kinase domain mutant "tmlr" with pyridone compound 19: 4-[(2- azanylpyrimidin-4-YL)AMINO]-~{N}-[4-(4-methylpiperazin-1-YL)PHENYL]- 2-oxidanylidene-1~{H}-pyridine-3-carboxamide
Analyse EGFR kinase domain mutant "tmlr" with pyridone compound 19: 4-[(2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EM6
- Type
- protein
- Length
- 301 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
- 5Q3, SO4
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 301 | 39% helix, 18% strand | P00533 |
Ligands and binding sites
- 5Q3 · 4-[(2-azanylpyrimidin-4-yl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.57 | 0.78 | 28 | 5Q3 |
| 2 | 181 | 0.55 | 0.79 | 20 | empty |
| 3 | 144 | 0.53 | 0.80 | 23 | empty |
Compared structures
- 5EM6 · EGFR kinase domain mutant TMLR" with pyridone compound 19… · 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 5EM6 · PDBe 5EM6 · UniProt P00533
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