MolNFT v1 · #36572 · protein
Crystal structure of human cytochrome P450 2D6
2F9Q: “Crystal structure of human cytochrome P450 2D6”. X-ray diffraction, 2 ligands (HEM, SO4), 18 pockets (best druggability 0.85). MolNFT v1 #36572 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2F9Q
- Type
- protein
- Length
- 1,810 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, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 454 | 52% helix, 8% strand | P10635 |
| B, D | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 451 | 51% helix, 8% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.85 | 0.90 | 76 | HEM |
| 2 | 610 | 0.85 | 0.89 | 84 | HEM |
| 3 | 897 | 0.84 | 0.86 | 114 | HEM |
| 4 | 758 | 0.84 | 0.87 | 100 | HEM |
| 5 | 789 | 0.79 | 0.82 | 77 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1189 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1096 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 1056 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1036 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 543 Ų buried · 11 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 2F9Q · PDBe 2F9Q · UniProt P10635
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