Research workbench
EGFR D770_N771INSNPG in complex with PD168393
Analyse EGFR D770_N771INSNPG in complex with PD168393 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LRM
- Type
- protein
- Length
- 1,472 residues
- Chains
- 5
- 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
- YUN
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 307 | 34% helix, 19% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 293 | 36% helix, 18% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 293 | 37% helix, 20% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 289 | 38% helix, 19% strand | P00533 |
| E | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 290 | 38% helix, 18% strand | P00533 |
Ligands and binding sites
- YUN · N-{4-[(3-bromophenyl)amino]quinazolin-6-yl}propanamide · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.74 | 0.78 | 97 | YUN |
| 2 | 630 | 0.72 | 0.80 | 59 | YUN |
| 3 | 626 | 0.72 | 0.80 | 72 | YUN |
| 4 | 505 | 0.70 | 0.80 | 40 | YUN |
| 5 | 297 | 0.67 | 0.82 | 31 | YUN |
Interfaces
4 interfaces between chains.
- B–C · 1160 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1132 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1070 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1048 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
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 4LRM · PDBe 4LRM · UniProt P00533
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