MolNFT v1 · #141034 · protein
Crystal structure of EGFR 696-1022 T790M in complex with ibrutinib
5YU9 · Epidermal growth factor receptor: “Crystal structure of EGFR 696-1022 T790M in complex with ibrutinib”. X-ray diffraction, 2 ligands (1E8, CL), 20 pockets (best druggability 0.86). MolNFT v1 #141034 on GenesisL1: 3D structure…
- PDB
- 5YU9
- Type
- protein
- Length
- 1,203 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
- 1E8, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 302 | 43% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 295 | 43% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 306 | 43% helix, 16% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 45% helix, 16% strand | P00533 |
Ligands and binding sites
- 1E8 · 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 3 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.86 | 0.88 | 85 | empty |
| 2 | 765 | 0.80 | 0.83 | 83 | 1E8 |
| 3 | 529 | 0.73 | 0.81 | 58 | 1E8 |
| 4 | 255 | 0.71 | 0.86 | 31 | 1E8 |
| 5 | 319 | 0.68 | 0.82 | 44 | 1E8 |
Interfaces
5 interfaces between chains.
- A–D · 633 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 538 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 336 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 256 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5YU9 · Crystal structure of EGFR 696-1022 T790M in complex with Ibrutinib · 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 B against A, TM-score 0.89
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 5YU9 · PDBe 5YU9 · UniProt P00533
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