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Crystal structure of human CYP3A4 bound to an inhibitor
Analyse Crystal structure of human CYP3A4 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
- 6BDI
- Type
- protein
- Length
- 462 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.57
- Source
- Homo sapiens
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.14.1, 1.14.13.67, 1.14.13.97
- UniProt
- P08684
- Ligands
- HEM, DEJ
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.57 · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.13.-, 1.14.13.157, 1.14.13.32, 1.14.14.1, 1.14.13.67, 1.14.13.97) | protein | 462 | 53% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- DEJ · Tert-butyl [(2S)-1-(1H-indol-3-yl)-3-{[(2R)-3-oxo-2-[(propan-2-yl)amino]-3-{[(pyridin-3-yl) methyl]amino}propyl]sulfanyl}propan-2-yl]carbamate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.86 | 0.87 | 78 | HEM, DEJ |
| 2 | 252 | 0.49 | 0.74 | 31 | empty |
| 3 | 137 | 0.48 | 0.78 | 23 | empty |
| 4 | 126 | 0.43 | 0.76 | 30 | 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 6BDI · PDBe 6BDI · UniProt P08684
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