MolNFT v1 · #180391 · protein
Inactive conformation of EGFR (T790M/V948R) kinase in complex with bi- 4020
7KY0 · Epidermal growth factor receptor: “Inactive conformation of EGFR (T790M/V948R) kinase in complex with bi- 4020”. X-ray diffraction, 1 ligand (XA4), 19 pockets (best druggability 0.81). MolNFT v1 #180391 on GenesisL1: 3D structure…
- PDB
- 7KY0
- Type
- protein
- Length
- 1,156 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
- XA4
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 42% 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 | 288 | 42% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 285 | 41% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 289 | 41% helix, 17% strand | P00533 |
Ligands and binding sites
- XA4 · (20R)-10,15,20-trimethyl-2-[(4-methylpiperazin-1-yl) methyl]-18,19,20,21-tetrahydro-15H,17H-12,8-(metheno) pyrazolo[3',4':2,3][1,5,10, 12]oxatriazacycloheptadecino[12,11-a]benzimidazol-7(6H)-one · ligand · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.81 | 0.88 | 79 | XA4 |
| 2 | 380 | 0.81 | 0.90 | 63 | XA4 |
| 3 | 308 | 0.79 | 0.89 | 29 | empty |
| 4 | 317 | 0.78 | 0.89 | 27 | empty |
| 5 | 363 | 0.78 | 0.88 | 56 | XA4 |
Interfaces
5 interfaces between chains.
- D–A · 1662 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1631 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 515 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7KY0 · Inactive conformation of EGFR (T790M/V948R) kinase in complex with BI-4020 · 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 0.91
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 7KY0 · PDBe 7KY0 · UniProt P00533
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