Research workbench
Human cytochrome P450 2D6 quinidine complex
Analyse Human cytochrome P450 2D6 quinidine complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WNU
- Type
- protein
- Length
- 1,804 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
- HEM, QDN, ZN
- Pockets
- 10 · 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 | 449 | 53% helix, 10% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 453 | 53% helix, 9% strand | P10635 |
| C | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 452 | 53% helix, 9% strand | P10635 |
| D | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 450 | 53% helix, 10% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- QDN · Quinidine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 5 copies · chains A, C, B, D
- GOL · Glycerol · additive · 10 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.86 | 0.87 | 100 | HEM, QDN, DMS, GOL |
| 2 | 1063 | 0.86 | 0.86 | 103 | HEM, QDN, DMS, GOL |
| 3 | 1143 | 0.85 | 0.86 | 102 | HEM, QDN, DMS, GOL |
| 4 | 1170 | 0.84 | 0.84 | 107 | HEM, QDN, DMS, GOL |
| 5 | 969 | 0.83 | 0.84 | 81 | empty |
Interfaces
4 interfaces between chains.
- B–C · 788 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 777 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 173 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 105 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- P10635 · AlphaFold monomer V2.0 prediction for cytochrome P450 2D6 (P10635) · a predicted model of the same protein · chain A 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 4WNU · PDBe 4WNU · UniProt P10635
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