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Competitive replacement of thioridazine by prinomastat in crystals of cytochrome P450 2D6
Analyse Competitive replacement of thioridazine by prinomastat in crystals of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TDA
- Type
- protein
- Length
- 1,846 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, PN0, ZN
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 467 | 52% helix, 9% strand | P10635 |
| B, D | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 456 | 54% helix, 9% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PN0 · Prinomastat · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 5 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.88 | 0.93 | 63 | HEM, PN0 |
| 2 | 536 | 0.87 | 0.93 | 63 | HEM, PN0 |
| 3 | 559 | 0.87 | 0.92 | 67 | HEM, PN0 |
| 4 | 1133 | 0.86 | 0.87 | 92 | HEM, PN0 |
| 5 | 901 | 0.84 | 0.85 | 84 | empty |
Interfaces
4 interfaces between chains.
- A–D · 861 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 835 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3TDA · Competitive replacement of thioridazine by prinomastat in crystals of cytochrome P450 2D6 · 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 0.99
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 3TDA · PDBe 3TDA · UniProt P10635
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