MolNFT v1 · #117907 · protein
EGFR kinase domain with pyridone compound 13: 4-[(2-methoxyphenyl) amino]-~{N}-[4-(4-methylpiperazin-1-YL)PHENYL]-2-oxidanylidene-1~{H}- pyridine-3-carboxamide
5EM8 · Epidermal growth factor receptor: “EGFR kinase domain with pyridone compound 13: 4-[(2-methoxyphenyl)…”. X-ray diffraction, 1 ligand (5Q4), 2 pockets (best druggability 0.61). MolNFT v1 #117907 on GenesisL1: 3D structure, binding…
- PDB
- 5EM8
- Type
- protein
- Length
- 303 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
- 5Q4
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 303 | 39% helix, 19% strand | P00533 |
Ligands and binding sites
- 5Q4 · 4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methylpiperazin-1-yl)phenyl]-2-oxidanylidene-1~{H}-pyridine-3-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.61 | 0.77 | 48 | 5Q4 |
| 2 | 144 | 0.51 | 0.79 | 21 | empty |
Compared structures
- 5EM8 · EGFR kinase domain with pyridone compound 13: 4-[(2-methoxyphenyl)amino]-~{N}-[4-(4-methyl… · 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 0.96
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 5EM8 · PDBe 5EM8 · UniProt P00533
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