Research workbench
Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(6)
Analyse Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(6) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X2F
- Type
- protein
- Length
- 1,224 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
- 7XU
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 301 | 43% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 312 | 41% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 43% helix, 16% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 309 | 43% helix, 16% strand | P00533 |
Ligands and binding sites
- 7XU · 9-cyclohexyl-N2-[4-(4-methylpiperazin-1-yl)phenyl]-N8-phenyl-purine-2,8-diamine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.81 | 0.84 | 82 | 7XU |
| 2 | 810 | 0.79 | 0.82 | 85 | 7XU |
| 3 | 668 | 0.78 | 0.83 | 86 | 7XU |
| 4 | 395 | 0.77 | 0.86 | 33 | empty |
| 5 | 352 | 0.77 | 0.87 | 29 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1610 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1599 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 373 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 307 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 22 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5X2F · Crystal structure of EGFR 696-1022 T790M/V948R in complex with SKLB(6) · 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 0.88
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 5X2F · PDBe 5X2F · UniProt P00533
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