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Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-CHLOROPHENYL)IMIDAZOLE
Analyse Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IBD
- Type
- protein
- Length
- 465 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B6
- EC
- 1.14.14.1
- UniProt
- P20813
- Ligands
- CM5, HEM, CPZ, SCN
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2B6 (EC 1.14.14.1) | protein | 465 | 54% helix, 10% strand | P20813 |
Ligands and binding sites
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- CPZ · 4-(4-chlorophenyl)imidazole · ligand · chains A
- SCN · Thiocyanate ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.88 | 0.91 | 89 | HEM, CPZ |
| 2 | 88 | 0.68 | 0.91 | 15 | CM5 |
| 3 | 72 | 0.48 | 0.83 | 19 | empty |
| 4 | 168 | 0.45 | 0.75 | 23 | empty |
| 5 | 67 | 0.37 | 0.78 | 12 | CM5 |
Compared structures
- 3IBD · Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P20813 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B6 (P20813) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P20813
- Elsewhere: RCSB PDB 3IBD · PDBe 3IBD · UniProt P20813
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