MolNFT v1 · #36703 · protein
Microsomal P450 2A6 with the inhibitor N,N-DIMETHYL(5- (pyridin-3-YL)FURAN-2-YL)METHANAMINE bound
2FDU · Cytochrome P450 2A6: “Microsomal P450 2A6 with the inhibitor N,N-DIMETHYL(5- (pyridin-3-YL)FURAN-2-YL)METHANAMINE bound”. X-ray diffraction, 3 ligands (HEM, D1G, SO4), 18 pockets (best druggability 0.85). MolNFT v1 #36703 on…
- PDB
- 2FDU
- Type
- protein
- Length
- 1,856 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2A6
- EC
- 1.14.14.1
- UniProt
- P11509
- Ligands
- HEM, D1G, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 465 | 54% helix, 11% strand | P11509 |
| B | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 463 | 54% helix, 10% strand | P11509 |
| C, D | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- D1G · N,N-dimethyl(5-(pyridin-3-yl)furan-2-yl)methanamine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.85 | 0.93 | 44 | HEM, D1G |
| 2 | 462 | 0.85 | 0.92 | 53 | HEM, D1G |
| 3 | 436 | 0.85 | 0.92 | 52 | HEM, D1G |
| 4 | 497 | 0.84 | 0.90 | 59 | HEM, D1G |
| 5 | 1129 | 0.77 | 0.78 | 57 | empty |
Interfaces
5 interfaces between chains.
- A–B · 693 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 421 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 403 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 180 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 163 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2FDU · Microsomal P450 2A6 with the inhibitor N,N-Dimethyl(5-(pyridin-3-yl)furan-2-yl)methanamine… · the same entry in another collection · chain D against D, TM-score 1.00
- P11509 · AlphaFold monomer V2.0 prediction for cytochrome P450 2A6 (P11509) · a predicted model of the same protein · chain D 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 P11509
- Elsewhere: RCSB PDB 2FDU · PDBe 2FDU · UniProt P11509
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