Research workbench
EGFR kinase domain in complex with mutant selective allosteric inhibitor
Analyse EGFR kinase domain in complex with mutant selective allosteric inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D41
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- 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
- ANP, 57N, MG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 43% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 42% helix, 17% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 57N · (2R)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-2-phenyl-N-(1,3-thiazol-2-yl)acetamide · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.83 | 0.85 | 62 | MG, ANP, 57N |
| 2 | 345 | 0.72 | 0.84 | 43 | MG, ANP |
| 3 | 217 | 0.59 | 0.81 | 26 | empty |
| 4 | 173 | 0.54 | 0.80 | 22 | empty |
| 5 | 148 | 0.52 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1661 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5D41 · EGFR kinase domain in complex with mutant selective allosteric inhibitor · 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 0.87
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 5D41 · PDBe 5D41 · UniProt P00533
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