MolNFT v1 · #145581 · protein
V308E mutant of cytochrome P450 2D6 complexed with thioridazine
6CSB: “V308E mutant of cytochrome P450 2D6 complexed with thioridazine”. X-ray diffraction, 4 ligands (RTZ, HEM, 2CV), 13 pockets (best druggability 0.86). MolNFT v1 #145581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6CSB
- Type
- protein
- Length
- 1,814 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2D6
- EC
- 1.14.14.1
- UniProt
- P10635
- Ligands
- RTZ, HEM, 2CV, ZN
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 452 | 54% helix, 10% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 455 | 54% helix, 10% strand | P10635 |
| C | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 454 | 53% helix, 10% strand | P10635 |
| D | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 453 | 53% helix, 10% strand | P10635 |
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
- 2CV · Hega-10 · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains B
- GOL · Glycerol · additive · chains C
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.86 | 0.87 | 94 | HEM, RTZ, 2CV |
| 2 | 1126 | 0.84 | 0.85 | 98 | HEM, RTZ |
| 3 | 1107 | 0.84 | 0.84 | 96 | HEM, RTZ, 2CV |
| 4 | 1187 | 0.84 | 0.84 | 98 | HEM, RTZ, 2CV |
| 5 | 1110 | 0.79 | 0.81 | 78 | empty |
Interfaces
4 interfaces between chains.
- B–C · 558 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 555 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 185 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 95 Ų buried · 0 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 6CSB · PDBe 6CSB · UniProt P10635
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