Research workbench
Crystal structure of EGFR(T790M/V948R) in complex with LN3753
Analyse Crystal structure of EGFR(T790M/V948R) in complex with LN3753 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WA2
- Type
- protein
- Length
- 1,230 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
- TOV, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | 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 | 302 | 41% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 43% helix, 16% strand | P00533 |
Ligands and binding sites
- TOV · N-(3-{5-[2-(acetylamino)pyridin-4-yl]-2-(methylsulfanyl)-1H-imidazol-4-yl}phenyl)-2-fluoro-5-hydroxybenzamide · ligand · 4 copies · chains D, A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 749 | 0.84 | 0.88 | 81 | TOV |
| 2 | 1161 | 0.83 | 0.83 | 109 | CL, TOV |
| 3 | 256 | 0.78 | 0.90 | 28 | empty |
| 4 | 344 | 0.77 | 0.87 | 42 | TOV, CL |
| 5 | 197 | 0.65 | 0.85 | 27 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1710 Ų buried · 30 hydrogen bonds · protein-protein
- D–A · 1659 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 477 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 381 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6WA2 · Crystal structure of EGFR(T790M/V948R) in complex with LN3753 · the same entry in another collection · chain C against C, 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 0.88
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 6WA2 · PDBe 6WA2 · UniProt P00533
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