Human cytochrome P450 2D6 with two thioridazines bound in active site

Structure

x-ray diffraction · 2 distinct chains · 53% helix, 10% strand (DSSP).

Ligands and binding sites

• RTZ · 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine · ligand · 8 copies · chains A, B, C, D
• HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
• ZN · Zinc ion · metal · 7 copies · chains A, C, B, D
• PO4 · Phosphate ion · ion · chains A
• GOL · Glycerol · additive · 7 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–D · 884 Ų buried · 16 hydrogen bonds · protein-protein
• B–C · 844 Ų buried · 14 hydrogen bonds · protein-protein
• A–C · 179 Ų buried · 3 hydrogen bonds · protein-protein
• B–D · 104 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 3TBG · Human cytochrome P450 2D6 with two thioridazines bound in active site · the same entry in another collection · chain D against D, TM-score 1.00
• P10635 · AlphaFold monomer V2.0 prediction for cytochrome P450 2D6 (P10635) · a predicted model of the same protein · chain C against A, TM-score 1.00

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 P10635
• Elsewhere: RCSB PDB 3TBG · PDBe 3TBG · UniProt P10635