Research workbench
Human CYP3A4 bound to a drug mibefradil
Analyse Human CYP3A4 bound to a drug mibefradil in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OO9
- Type
- protein
- Length
- 460 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 3A4
- EC
- 1.14.14.-, 1.14.14.56, 1.14.14.73, 1.14.14.55
- UniProt
- P08684
- Ligands
- HEM, MWV
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 3A4 (EC 1.14.14.-, 1.14.14.56, 1.14.14.73, 1.14.14.55) | protein | 460 | 50% helix, 9% strand | P08684 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- MWV · (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl) amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.87 | 0.88 | 75 | HEM, MWV |
| 2 | 172 | 0.52 | 0.78 | 24 | empty |
| 3 | 191 | 0.47 | 0.74 | 22 | EDO |
| 4 | 92 | 0.37 | 0.75 | 16 | 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 6OO9 · PDBe 6OO9 · UniProt P08684
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