Research workbench
Crystal structure of EGFR 696-1022 T790M in complex with ql-X138
Analyse Crystal structure of EGFR 696-1022 T790M in complex with ql-X138 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WD5
- Type
- protein
- Length
- 611 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
- 3LH, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 307 | 37% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 304 | 37% helix, 17% strand | P00533 |
Ligands and binding sites
- 3LH · N-{2-methyl-5-[2-oxo-9-(1H-pyrazol-4-yl)benzo[h][1,6]naphthyridin-1(2H)-yl]phenyl}propanamide · ligand · chains A
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.70 | 0.81 | 45 | empty |
| 2 | 393 | 0.61 | 0.77 | 38 | empty |
| 3 | 416 | 0.61 | 0.76 | 51 | 3LH |
| 4 | 174 | 0.52 | 0.78 | 25 | empty |
| 5 | 121 | 0.46 | 0.78 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4WD5 · Crystal structure of EGFR 696-1022 T790M in complex with QL-X138 · 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 0.97
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 4WD5 · PDBe 4WD5 · UniProt P00533
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