Research workbench
Crystal structure of EGFR with mutant-selective dihydrodibenzodiazepinone allosteric inhibitor
Analyse Crystal structure of EGFR with mutant-selective dihydrodibenzodiazepinone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P1D
- Type
- protein
- Length
- 1,196 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, NQ1, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 295 | 43% helix, 16% strand | P00533 |
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 309 | 41% helix, 16% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 42% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 292 | 43% helix, 17% strand | P00533 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains D, A, B, C
- NQ1 · 10-benzyl-8-fluoro-5,10-dihydro-11H-dibenzo[b,e][1, 4]diazepin-11-one · ligand · 3 copies · chains D, 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
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.83 | 0.85 | 98 | ANP, MG |
| 2 | 548 | 0.79 | 0.85 | 63 | NQ1, ANP, MG |
| 3 | 804 | 0.79 | 0.82 | 67 | empty |
| 4 | 370 | 0.77 | 0.86 | 42 | ANP, NQ1, MG |
| 5 | 397 | 0.76 | 0.86 | 49 | NQ1, ANP, MG |
Interfaces
5 interfaces between chains.
- A–B · 641 Ų buried · 4 hydrogen bonds · protein-protein
- D–B · 382 Ų buried · 6 hydrogen bonds · protein-protein
- D–C · 362 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 319 Ų buried · 5 hydrogen bonds · protein-protein
- D–A · 277 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6P1D · Crystal structure of EGFR with mutant-selective dihydrodibenzodiazepi allosteric inhibitor · 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 C 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 6P1D · PDBe 6P1D · UniProt P00533
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