Research workbench
Human cytochrome P450 2D6 thioridazine complex
Analyse Human cytochrome P450 2D6 thioridazine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WNW
- Type
- protein
- Length
- 913 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2D6
- EC
- 1.14.14.1
- UniProt
- P10635
- Ligands
- HEM, RTZ, NA, NI
- Pockets
- 13 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 461 | 51% helix, 9% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 452 | 51% helix, 9% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- RTZ · 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.90 | 0.92 | 87 | HEM, RTZ, NA |
| 2 | 856 | 0.89 | 0.92 | 88 | HEM, RTZ, NA |
| 3 | 821 | 0.73 | 0.78 | 66 | empty |
| 4 | 253 | 0.58 | 0.78 | 31 | empty |
| 5 | 177 | 0.51 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1243 Ų buried · 9 hydrogen bonds · protein-protein
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 P10635
- Elsewhere: RCSB PDB 4WNW · PDBe 4WNW · UniProt P10635
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