Research workbench
Structure of EGFR_D770_N771INSNPG/V948R in complex with covalent inhibitor osimertinib.
Analyse Structure of EGFR_D770_N771INSNPG/V948R in complex with covalent inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LGS
- Type
- protein
- Length
- 1,131 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
- Q6K
- Pockets
- 12 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 283 | 35% helix, 20% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 286 | 37% helix, 20% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 283 | 35% helix, 21% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 279 | 36% helix, 22% strand | P00533 |
Ligands and binding sites
- Q6K · ~{N}-[2-[2-(dimethylamino)ethyl-methyl-amino]-4-methoxy-5-[[4-(1-methylindol-3-yl)pyrimidin-2-yl]amino]phenyl]propanamide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.72 | 0.77 | 82 | Q6K |
| 2 | 748 | 0.71 | 0.77 | 77 | Q6K |
| 3 | 359 | 0.69 | 0.82 | 39 | EDO |
| 4 | 512 | 0.68 | 0.78 | 49 | Q6K |
| 5 | 473 | 0.66 | 0.78 | 53 | Q6K |
Interfaces
5 interfaces between chains.
- B–D · 921 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 108 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7LGS · Structure of EGFR_D770_N771insNPG/V948R in complex with covalent inhibitor Osimertinib. · 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 C 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 7LGS · PDBe 7LGS · UniProt P00533
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