MolNFT v1 · #36707 · protein
Microsomal P450 2A6 with the inhibitor adrithiol bound
2FDY · Cytochrome P450 2A6: “Microsomal P450 2A6 with the inhibitor adrithiol bound”. X-ray diffraction, 3 ligands (HEM, D4G, SO4), 16 pockets (best druggability 0.86). MolNFT v1 #36707 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2FDY
- Type
- protein
- Length
- 1,857 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, D4G, SO4
- Pockets
- 16 · best druggability 0.86
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 | 52% helix, 10% strand | P11509 |
| B | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 464 | 52% helix, 10% strand | P11509 |
| C, D | Cytochrome P450 2A6 (EC 1.14.14.1) | protein | 464 | 54% helix, 10% strand | P11509 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- D4G · 4,4'-dipyridyl disulfide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.86 | 0.93 | 50 | HEM, D4G |
| 2 | 440 | 0.86 | 0.93 | 48 | HEM, D4G |
| 3 | 436 | 0.86 | 0.93 | 49 | HEM, D4G |
| 4 | 471 | 0.86 | 0.92 | 56 | HEM, D4G |
| 5 | 1131 | 0.77 | 0.78 | 55 | empty |
Interfaces
5 interfaces between chains.
- A–B · 826 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 422 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 402 Ų buried · 2 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
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 2FDY · PDBe 2FDY · UniProt P11509
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