Research workbench
Crystal structure of EGFR 696-1022 T790M in complex with lxx-6-26
Analyse Crystal structure of EGFR 696-1022 T790M in complex with lxx-6-26 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GTY
- Type
- protein
- Length
- 2,384 residues
- Chains
- 8
- 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
- 816
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 39% helix, 15% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 299 | 39% helix, 14% strand | P00533 |
| D, E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 41% helix, 16% strand | P00533 |
| F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 39% helix, 15% strand | P00533 |
| G | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 299 | 39% helix, 15% strand | P00533 |
| H | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 38% helix, 14% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 295 | 38% helix, 16% strand | P00533 |
Ligands and binding sites
- 816 · 1-[(3R)-3-[4-azanyl-3-[3-chloranyl-4-[(6-methylpyridin-2-yl)methoxy]phenyl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]prop-2-en-1-one · ligand · 8 copies · chains A, B, D, E, F, G, H, C
- EDO · 1,2-ethanediol · additive · 4 copies · chains G, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.86 | 0.87 | 80 | empty |
| 2 | 1188 | 0.85 | 0.86 | 88 | empty |
| 3 | 827 | 0.84 | 0.86 | 55 | empty |
| 4 | 940 | 0.81 | 0.83 | 93 | 816 |
| 5 | 314 | 0.76 | 0.87 | 35 | 816 |
Interfaces
13 interfaces between chains.
- F–G · 708 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 696 Ų buried · 2 hydrogen bonds · protein-protein
- E–C · 690 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 628 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 598 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5GTY · Crystal structure of EGFR 696-1022 T790M in complex with LXX-6-26 · 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 H 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 5GTY · PDBe 5GTY · UniProt P00533
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