Research workbench
EGFR(T790M/V948R) in complex with LN2380
Analyse EGFR(T790M/V948R) in complex with LN2380 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V6O
- Type
- protein
- Length
- 2,427 residues
- Chains
- 8
- 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
- QQM, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 314 | 43% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 307 | 43% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 43% helix, 17% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 303 | 42% helix, 17% strand | P00533 |
| F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 299 | 43% helix, 16% strand | P00533 |
| G | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 294 | 43% helix, 17% strand | P00533 |
| H | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 299 | 43% helix, 17% strand | P00533 |
Ligands and binding sites
- QQM · N-[3-({4-[4-(4-fluorophenyl)-2-(3-hydroxypropyl)-1H-imidazol-5-yl]pyridin-2-yl}amino)-4-methoxyphenyl]propanamide · ligand · 8 copies · chains D, A, B, C, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains D, A, B, C, E, F, G, H
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 | 1136 | 0.84 | 0.85 | 125 | CL, QQM |
| 2 | 878 | 0.83 | 0.85 | 88 | QQM |
| 3 | 829 | 0.80 | 0.83 | 97 | QQM, CL |
| 4 | 608 | 0.80 | 0.85 | 82 | CL, QQM |
| 5 | 350 | 0.77 | 0.87 | 29 | empty |
Interfaces
14 interfaces between chains.
- A–F · 1693 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1668 Ų buried · 19 hydrogen bonds · protein-protein
- B–H · 531 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 424 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 389 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
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 6V6O · PDBe 6V6O · UniProt P00533
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