Research workbench
Microsomal P450 2A6 with the inhibitor N-METHYL(5-(pyridin- 3-YL)FURAN-2-YL)METHANAMINE bound
Analyse Microsomal P450 2A6 with the inhibitor N-METHYL(5-(pyridin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FDV
- Type
- protein
- Length
- 1,858 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, D2G, SO4
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 465 | 53% helix, 10% strand | P11509 |
| B | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 465 | 54% helix, 11% strand | P11509 |
| C, D | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 464 | 53% helix, 11% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- D2G · N-methyl(5-(pyridin-3-yl)furan-2-yl)methanamine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.86 | 0.94 | 46 | HEM, D2G |
| 2 | 427 | 0.86 | 0.93 | 49 | HEM, D2G |
| 3 | 415 | 0.86 | 0.94 | 48 | HEM, D2G |
| 4 | 460 | 0.85 | 0.92 | 58 | SO4, HEM, D2G |
| 5 | 1108 | 0.79 | 0.81 | 98 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 718 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 418 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 393 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 185 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2FDV · Microsomal P450 2A6 with the inhibitor N-Methyl(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 C 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 2FDV · PDBe 2FDV · UniProt P11509
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