MolNFT v1 · #179176 · protein
EGFR kinase (T790M/V948R) in complex with osimertinib and EAI045
7JXM · Epidermal growth factor receptor: “EGFR kinase (T790M/V948R) in complex with osimertinib and EAI045”. X-ray diffraction, 4 ligands (ANP, 9LL, YY3), 20 pockets (best druggability 0.82). MolNFT v1 #179176 on GenesisL1: 3D structure…
- PDB
- 7JXM
- Type
- protein
- Length
- 1,159 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
- ANP, 9LL, YY3, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 291 | 43% helix, 17% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 287 | 43% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 285 | 43% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 296 | 42% helix, 17% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 3 copies · chains D, A, C
- 9LL · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide · ligand · 2 copies · chains D, B
- YY3 · N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains D, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.82 | 0.85 | 83 | ANP, MG, 9LL |
| 2 | 724 | 0.76 | 0.81 | 72 | ANP, MG |
| 3 | 471 | 0.75 | 0.83 | 43 | YY3, 9LL |
| 4 | 288 | 0.69 | 0.83 | 37 | ANP, MG |
| 5 | 473 | 0.68 | 0.79 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–C · 435 Ų buried · 5 hydrogen bonds · protein-protein
- D–C · 364 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 347 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 291 Ų buried · 1 hydrogen bond · protein-protein
- C–B · 268 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7JXM · EGFR kinase (T790M/V948R) in complex with osimertinib and EAI045 · the same entry in another collection · chain B against B, 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 0.91
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 7JXM · PDBe 7JXM · UniProt P00533
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