Research workbench
Cytochrome P450 3A4 bound to an inhibitor
Analyse Cytochrome P450 3A4 bound to an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D75
- 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
- PK9, HEM
- Pockets
- 5 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 51% helix, 9% strand | P08684 |
Ligands and binding sites
- PK9 · tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate · ligand · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.87 | 0.88 | 76 | PK9, HEM |
| 2 | 199 | 0.47 | 0.74 | 25 | empty |
| 3 | 96 | 0.46 | 0.80 | 21 | empty |
| 4 | 106 | 0.45 | 0.78 | 28 | empty |
| 5 | 76 | 0.33 | 0.75 | 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 4D75 · PDBe 4D75 · UniProt P08684
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