MolNFT v1 · #179174 · protein
EGFR kinase (T790M/V948R) in complex with pf-06747775 and jbj-04-125- 02
7JXK · Epidermal growth factor receptor: “EGFR kinase (T790M/V948R) in complex with pf-06747775 and jbj-04-125- 02”. X-ray diffraction, 4 ligands (JBJ, 8BS, ANP), 20 pockets (best druggability 0.82). MolNFT v1 #179174 on GenesisL1: 3D…
- PDB
- 7JXK
- Type
- protein
- Length
- 1,748 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, 8BS, ANP, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 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 | 294 | 43% helix, 17% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 293 | 43% helix, 17% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 42% helix, 17% strand | P00533 |
| F | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 43% helix, 17% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 287 | 43% helix, 17% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 290 | 44% helix, 15% 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 · 5 copies · chains D, A, C, F, E
- 8BS · N-[(3R,4R)-4-fluoro-1-{6-[(3-methoxy-1-methyl-1H-pyrazol-4-yl)amino]-9-methyl-9H-purin-2-yl}pyrrolidin-3-yl]propanamide · ligand · 4 copies · chains A, D, C, F, E
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains D, A, B
- MG · Magnesium ion · metal · 2 copies · chains D, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.82 | 0.83 | 108 | 8BS, JBJ |
| 2 | 1040 | 0.81 | 0.82 | 80 | ANP, MG |
| 3 | 326 | 0.79 | 0.89 | 29 | empty |
| 4 | 352 | 0.77 | 0.87 | 30 | empty |
| 5 | 471 | 0.76 | 0.84 | 51 | ANP, MG, JBJ |
Interfaces
10 interfaces between chains.
- D–A · 1692 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 1668 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 444 Ų buried · 8 hydrogen bonds · protein-protein
- D–C · 409 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 360 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7JXK · EGFR kinase (T790M/V948R) in complex with PF-06747775 and JBJ-04-125-02 · 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 E 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 7JXK · PDBe 7JXK · UniProt P00533
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