Research workbench
EGFR with an allosteric inhibitor
Analyse EGFR with an allosteric inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DUK
- Type
- protein
- Length
- 1,800 residues
- Chains
- 6
- 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, JBJ, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 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 | 306 | 42% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 296 | 43% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 295 | 43% helix, 18% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 307 | 42% helix, 16% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 298 | 43% helix, 16% strand | P00533 |
| F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 298 | 41% helix, 16% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- JBJ · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{1-oxo-6-[4-(piperazin-1-yl)phenyl]-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.84 | 0.86 | 76 | MG, ANP, JBJ |
| 2 | 1130 | 0.82 | 0.83 | 100 | MG, ANP, JBJ |
| 3 | 895 | 0.82 | 0.83 | 82 | MG, ANP, JBJ |
| 4 | 1049 | 0.80 | 0.81 | 95 | MG, ANP, JBJ |
| 5 | 360 | 0.79 | 0.89 | 28 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1631 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1626 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1587 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 403 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 314 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 6DUK · PDBe 6DUK · UniProt P00533
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