Research workbench
Cytochrome P450 3A4 bound to imidazole and an inhibitor
Analyse Cytochrome P450 3A4 bound to imidazole and an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D6Z
- Type
- protein
- Length
- 460 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97
- UniProt
- P08684
- Ligands
- HEM, PK9
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.157, 1.14.13.32, 1.14.13.67, 1.14.13.97) | protein | 460 | 52% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- PK9 · tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate · ligand · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.87 | 0.87 | 75 | HEM, PK9, IMD |
| 2 | 154 | 0.51 | 0.79 | 25 | empty |
| 3 | 229 | 0.48 | 0.74 | 31 | empty |
| 4 | 100 | 0.36 | 0.74 | 20 | GOL |
| 5 | 51 | 0.34 | 0.78 | 17 | empty |
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 P08684
- Elsewhere: RCSB PDB 4D6Z · PDBe 4D6Z · UniProt P08684
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