Research workbench
Crystal structure of EGFR-T790M/V948R in complex with tak-788
Analyse Crystal structure of EGFR-T790M/V948R in complex with tak-788 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A6K
- Type
- protein
- Length
- 1,043 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
- R28, SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 266 | 41% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 260 | 42% helix, 19% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 262 | 45% helix, 18% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 255 | 42% helix, 18% strand | P00533 |
Ligands and binding sites
- R28 · propan-2-yl 2-[[4-[2-(dimethylamino)ethyl-methyl-amino]-2-methoxy-5-(propanoylamino)phenyl]amino]-4-(1-methylindol-3-yl)pyrimidine-5-carboxylate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.71 | 0.76 | 69 | empty |
| 2 | 390 | 0.68 | 0.80 | 44 | R28 |
| 3 | 477 | 0.64 | 0.77 | 49 | R28, SO4 |
| 4 | 330 | 0.63 | 0.79 | 37 | R28 |
| 5 | 273 | 0.62 | 0.80 | 34 | R28, SO4 |
Interfaces
4 interfaces between chains.
- B–D · 471 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 274 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 231 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 207 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7A6K · Crystal Structure of EGFR-T790M/V948R in Complex with TAK-788 · 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 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 7A6K · PDBe 7A6K · UniProt P00533
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