MolNFT v1 · #179179 · protein
EGFR kinase (T790M/V948R) in complex with osimertinib and jbj-04-125- 02
7JXP · Epidermal growth factor receptor: “EGFR kinase (T790M/V948R) in complex with osimertinib and jbj-04-125- 02”. X-ray diffraction, 4 ligands (JBJ, ANP, YY3), 20 pockets (best druggability 0.85). MolNFT v1 #179179 on GenesisL1: 3D…
- PDB
- 7JXP
- Type
- protein
- Length
- 1,783 residues
- Chains
- 6
- 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
- JBJ, ANP, YY3, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 294 | 43% helix, 17% strand | P00533 |
| A, B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 308 | 41% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 44% helix, 17% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 287 | 42% helix, 17% strand | P00533 |
Ligands and binding sites
- JBJ · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{1-oxo-6-[4-(piperazin-1-yl)phenyl]-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide · ligand · 6 copies · chains D, A, C, F, B, E
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains D, A, F, 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 · 2 copies · chains C, E
- MG · Magnesium ion · metal · 4 copies · chains D, A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.85 | 0.87 | 85 | ANP, MG, JBJ |
| 2 | 697 | 0.85 | 0.88 | 81 | ANP, MG, JBJ |
| 3 | 796 | 0.81 | 0.83 | 83 | ANP, MG, JBJ |
| 4 | 328 | 0.79 | 0.89 | 30 | empty |
| 5 | 379 | 0.77 | 0.87 | 47 | ANP, JBJ |
Interfaces
10 interfaces between chains.
- A–E · 1679 Ų buried · 20 hydrogen bonds · protein-protein
- D–B · 580 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 364 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 360 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7JXP · EGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-04-125-02 · the same entry in another collection · chain E against E, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 7JXP · PDBe 7JXP · UniProt P00533
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