Research workbench
Crystal structure of EGFR 696-1022 T790M mutant covalently binding to WZ4002
Analyse Crystal structure of EGFR 696-1022 T790M mutant covalently binding to WZ4002 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IKA
- Type
- protein
- Length
- 620 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
- 0UN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 310 | 37% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 310 | 41% helix, 17% strand | P00533 |
Ligands and binding sites
- 0UN · N-{3-[(5-chloro-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)oxy]phenyl}prop-2-enamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.71 | 0.77 | 86 | 0UN |
| 2 | 317 | 0.66 | 0.81 | 29 | empty |
| 3 | 158 | 0.51 | 0.79 | 22 | empty |
| 4 | 87 | 0.36 | 0.76 | 25 | empty |
| 5 | 92 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1028 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3IKA · Crystal Structure of EGFR 696-1022 T790M Mutant Covalently Binding to WZ4002 · 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 3IKA · PDBe 3IKA · UniProt P00533
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