MolNFT v1 · #143913 · protein
Crystal structure of human CYP3A4 bound to an inhibitor
6BDM · Cytochrome P450 3A4: “Crystal structure of human CYP3A4 bound to an inhibitor”. X-ray diffraction, 2 ligands (HEM, Y83), 4 pockets (best druggability 0.84). MolNFT v1 #143913 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6BDM
- Type
- protein
- Length
- 456 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, Y83
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 52% 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 | 456 | 52% helix, 10% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- Y83 · Tert-butyl [(2S)-1-(1H-indol-3-yl)-3-{[(2S)-3-oxo-2-(phenylamino)-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 | 1196 | 0.84 | 0.84 | 85 | HEM, Y83 |
| 2 | 214 | 0.50 | 0.75 | 26 | empty |
| 3 | 147 | 0.47 | 0.77 | 27 | empty |
| 4 | 51 | 0.42 | 0.83 | 14 | 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 6BDM · PDBe 6BDM · UniProt P08684
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