MolNFT v1 · #166947 · protein
EGFR(T790M/V948R) in complex with LN2899
6V66 · Epidermal growth factor receptor: “EGFR(T790M/V948R) in complex with LN2899”. X-ray diffraction, 2 ligands (QP1, CL), 20 pockets (best druggability 0.83). MolNFT v1 #166947 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6V66
- Type
- protein
- Length
- 1,229 residues
- Chains
- 4
- 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
- QP1, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 314 | 43% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 42% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 299 | 42% helix, 16% strand | P00533 |
Ligands and binding sites
- QP1 · N-{3-[(4-{4-(4-fluorophenyl)-2-[(2-methoxyethyl) sulfanyl]-1H-imidazol-5-yl}pyridin-2-yl)amino]-4-methoxyphenyl}propanamide · ligand · 4 copies · chains D, A, B, C
- CL · Chloride ion · ion · 4 copies · chains D, A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.83 | 0.85 | 87 | QP1 |
| 2 | 694 | 0.81 | 0.84 | 65 | QP1 |
| 3 | 328 | 0.80 | 0.90 | 29 | empty |
| 4 | 501 | 0.78 | 0.85 | 62 | QP1 |
| 5 | 415 | 0.70 | 0.81 | 54 | QP1, CL |
Interfaces
6 interfaces between chains.
- A–C · 1659 Ų buried · 20 hydrogen bonds · protein-protein
- D–B · 1627 Ų buried · 20 hydrogen bonds · protein-protein
- D–A · 459 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 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 6V66 · PDBe 6V66 · UniProt P00533
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