Single ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole

Structure

x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).

Ligands and binding sites

• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• PB2 · 1-(biphenyl-4-ylmethyl)-1H-imidazole · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–B · 3989 Ų buried · 37 hydrogen bonds · protein-protein
• A–C · 454 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 160 Ų buried · 2 hydrogen bonds · protein-protein
• A–D · 105 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 3G93 · Single ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the… · the same entry in another collection · chain D against D, TM-score 1.00
• P00178 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B4 (P00178) · a predicted model of the same protein · chain B against A, TM-score 0.88

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 P00178
• Elsewhere: RCSB PDB 3G93 · PDBe 3G93 · UniProt P00178