MolNFT v1 · #94619 · protein
Structure of T790M EGFR kinase domain co-crystallized with dacomitinib
4I24 · Epidermal growth factor receptor: “Structure of T790M EGFR kinase domain co-crystallized with dacomitinib”. X-ray diffraction, 1 ligand (1C9), 7 pockets (best druggability 0.83). MolNFT v1 #94619 on GenesisL1: 3D structure, binding…
- PDB
- 4I24
- Type
- protein
- Length
- 599 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
- 1C9
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 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 | 295 | 43% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 304 | 41% helix, 16% strand | P00533 |
Ligands and binding sites
- 1C9 · (2E)-N-{4-[(3-chloro-4-fluorophenyl)amino]-7-methoxyquinazolin-6-yl}-4-(piperidin-1-yl)but-2-enamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.83 | 0.87 | 67 | 1C9 |
| 2 | 318 | 0.74 | 0.86 | 47 | 1C9 |
| 3 | 206 | 0.58 | 0.80 | 23 | empty |
| 4 | 202 | 0.57 | 0.80 | 23 | empty |
| 5 | 77 | 0.43 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1567 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4I24 · Structure of T790M EGFR kinase domain co-crystallized with dacomitinib · 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 0.87
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 4I24 · PDBe 4I24 · UniProt P00533
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