MolNFT v1 · #166957 · protein
EGFR(T790M/V948R) in complex with LN2057
6V6K · Epidermal growth factor receptor: “EGFR(T790M/V948R) in complex with LN2057”. X-ray diffraction, 2 ligands (QQJ, CL), 20 pockets (best druggability 0.81). MolNFT v1 #166957 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6V6K
- Type
- protein
- Length
- 2,454 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
- QQJ, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, G, H | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 314 | 40% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 42% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 301 | 43% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 42% helix, 16% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 303 | 41% helix, 16% strand | P00533 |
| F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 306 | 42% helix, 17% strand | P00533 |
Ligands and binding sites
- QQJ · N-[3-({4-[4-(4-fluorophenyl)-2-(methylsulfanyl)-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 | 638 | 0.81 | 0.86 | 69 | QQJ |
| 2 | 725 | 0.81 | 0.84 | 61 | QQJ |
| 3 | 867 | 0.80 | 0.82 | 78 | QQJ |
| 4 | 914 | 0.77 | 0.80 | 90 | QQJ |
| 5 | 235 | 0.77 | 0.90 | 36 | CL, QQJ |
Interfaces
14 interfaces between chains.
- E–F · 1670 Ų buried · 18 hydrogen bonds · protein-protein
- A–H · 1669 Ų buried · 23 hydrogen bonds · protein-protein
- C–G · 531 Ų buried · 7 hydrogen bonds · protein-protein
- F–H · 464 Ų buried · 7 hydrogen bonds · protein-protein
- D–G · 434 Ų buried · 2 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 6V6K · PDBe 6V6K · UniProt P00533
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