MolNFT v1 · #180963 · protein
EGFR (T79M/V948R) in complex with naquotinib and an allosteric inhibitor
7LG8 · Epidermal growth factor receptor: “EGFR (T79M/V948R) in complex with naquotinib and an allosteric inhibitor”. X-ray diffraction, 2 ligands (VNS, 8RC), 9 pockets (best druggability 0.79). MolNFT v1 #180963 on GenesisL1: 3D structure…
- PDB
- 7LG8
- Type
- protein
- Length
- 1,100 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
- VNS, 8RC
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 280 | 39% helix, 20% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 275 | 39% helix, 19% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 274 | 40% helix, 18% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 271 | 40% helix, 18% strand | P00533 |
Ligands and binding sites
- VNS · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{6-[4-(1-methylpiperidin-4-yl)phenyl]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide · ligand · 4 copies · chains A, B, C, D
- 8RC · 6-ethyl-3-[[4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]-5-[(3R)-1-prop-2-enoylpyrrolidin-3-yl]oxy-pyrazine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 902 | 0.79 | 0.81 | 80 | VNS, 8RC |
| 2 | 1005 | 0.78 | 0.79 | 89 | VNS, 8RC |
| 3 | 590 | 0.75 | 0.82 | 53 | VNS, 8RC |
| 4 | 705 | 0.73 | 0.79 | 60 | VNS, 8RC |
| 5 | 246 | 0.46 | 0.73 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 305 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 211 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 168 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 147 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7LG8 · EGFR (T79M/V948R) in complex with naquotinib and an allosteric inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 7LG8 · PDBe 7LG8 · UniProt P00533
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