Research workbench
Crystal structure of EGFR-T790M/V948R in complex with mavelertinib and EAI001
Analyse Crystal structure of EGFR-T790M/V948R in complex with mavelertinib and EAI001 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z4D
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- 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
- 8BS, 57N, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 269 | 41% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 270 | 42% helix, 19% strand | P00533 |
Ligands and binding sites
- 8BS · N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide · ligand · 2 copies · chains A, B
- 57N · (2R)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-2-phenyl-N-(1,3-thiazol-2-yl)acetamide · ligand · chains B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1189 | 0.80 | 0.82 | 133 | 8BS, SO4, 57N |
| 2 | 300 | 0.54 | 0.75 | 39 | empty |
| 3 | 142 | 0.47 | 0.77 | 23 | empty |
| 4 | 71 | 0.34 | 0.76 | 15 | empty |
| 5 | 58 | 0.32 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1237 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6Z4D · Crystal Structure of EGFR-T790M/V948R in Complex with Mavelertinib and EAI001 · the same entry in another collection · chain A against A, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A 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 6Z4D · PDBe 6Z4D · UniProt P00533
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