Research workbench
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
- 6BD8
- Type
- protein
- Length
- 457 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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, D81
- Pockets
- 4 · best druggability 0.86
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.-, 1.14.13.157, 1.14.13.32, 1.14.14.1, 1.14.13.67, 1.14.13.97) | protein | 457 | 52% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- D81 · S-{(2S)-2-[(1-tert-butoxyethenyl)amino]-3-phenylpropyl}-N~2~-cyclopentyl-N-[(pyridin-3-yl) methyl]-L-cysteinamide · 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 | 1098 | 0.86 | 0.87 | 79 | HEM, D81 |
| 2 | 201 | 0.45 | 0.73 | 23 | empty |
| 3 | 109 | 0.45 | 0.78 | 24 | empty |
| 4 | 124 | 0.44 | 0.77 | 28 | 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 6BD8 · PDBe 6BD8 · UniProt P08684
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