Research workbench
EGFR kinase (T790M/V948R) in complex with allosteric inhibitor jbj-09- 063
Analyse EGFR kinase (T790M/V948R) in complex with allosteric inhibitor jbj-09- 063 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JXQ
- Type
- protein
- Length
- 1,189 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, VNS, MG
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 298 | 45% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 296 | 43% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 297 | 43% helix, 18% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains D, A, B, C
- VNS · (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{6-[4-(1-methylpiperidin-4-yl)phenyl]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide · ligand · 4 copies · chains D, A, B, C
- MG · Magnesium ion · metal · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 830 | 0.79 | 0.82 | 81 | MG, VNS, ANP |
| 2 | 804 | 0.77 | 0.81 | 87 | MG, ANP, VNS |
| 3 | 531 | 0.77 | 0.84 | 52 | MG, ANP, VNS |
| 4 | 700 | 0.76 | 0.81 | 71 | MG, VNS, ANP |
| 5 | 241 | 0.48 | 0.74 | 28 | empty |
Interfaces
5 interfaces between chains.
- B–C · 182 Ų buried · 1 hydrogen bond · protein-protein
- D–B · 167 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
- D–A · 125 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 112 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7JXQ · EGFR kinase (T790M/V948R) in complex with allosteric inhibitor JBJ-09-063 · the same entry in another collection · chain C against C, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain B 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 7JXQ · PDBe 7JXQ · UniProt P00533
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