MolNFT v1 · #160036 · protein
EGFR in complex with a dihydrodibenzodiazepinone allosteric inhibitor.
6P8Q · Epidermal growth factor receptor: “EGFR in complex with a dihydrodibenzodiazepinone allosteric inhibitor.”. X-ray diffraction, 4 ligands (O57, AMP, ANP), 19 pockets (best druggability 0.88). MolNFT v1 #160036 on GenesisL1: 3D…
- PDB
- 6P8Q
- Type
- protein
- Length
- 1,221 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
- O57, AMP, ANP, MG
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 309 | 44% helix, 15% strand | P00533 |
| B | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 300 | 45% helix, 16% strand | P00533 |
| C | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 316 | 45% helix, 15% strand | P00533 |
| D | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 296 | 45% helix, 16% strand | P00533 |
Ligands and binding sites
- O57 · 10-benzyl-2-fluoro-5,10-dihydro-11H-dibenzo[b,e][1, 4]diazepin-11-one · ligand · 4 copies · chains A, B, C, D
- AMP · Adenosine monophosphate · ligand · 3 copies · chains B, A, C, D
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.88 | 0.89 | 122 | AMP, O57, MG, EDO |
| 2 | 242 | 0.85 | 0.97 | 26 | empty |
| 3 | 1039 | 0.83 | 0.84 | 107 | AMP, O57, MG |
| 4 | 447 | 0.79 | 0.87 | 56 | AMP, O57, MG |
| 5 | 384 | 0.78 | 0.87 | 42 | ANP, O57, MG |
Interfaces
5 interfaces between chains.
- A–B · 1679 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1615 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1088 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 191 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6P8Q · EGFR in complex with a dihydrodibenzodiazepi allosteric inhibitor. · the same entry in another collection · chain D against D, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain D 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 6P8Q · PDBe 6P8Q · UniProt P00533
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