MolNFT v1 · #134803 · protein
Structure of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex
5TFU: “Structure of cytochrome P450 2D6 (CYP2D6) BACE1 inhibitor complex”. X-ray diffraction, 3 ligands (HEM, P6M, ZN), 10 pockets (best druggability 0.87). MolNFT v1 #134803 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TFU
- Type
- protein
- Length
- 1,805 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, P6M, ZN
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 451 | 54% helix, 9% strand | P10635 |
| B | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 451 | 54% helix, 10% strand | P10635 |
| C | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 450 | 53% helix, 9% strand | P10635 |
| D | Cytochrome P450 2D6 (EC 1.14.14.1) | protein | 453 | 53% helix, 10% strand | P10635 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- P6M · (4S,6R)-4-[2,4-difluoro-5-({[1-(trifluoromethyl) cyclopropyl]amino}methyl)phenyl]-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-2-amine · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.87 | 0.88 | 100 | HEM, P6M |
| 2 | 1059 | 0.86 | 0.87 | 93 | HEM, P6M |
| 3 | 1103 | 0.86 | 0.86 | 100 | HEM, P6M |
| 4 | 1115 | 0.85 | 0.86 | 102 | HEM, P6M |
| 5 | 840 | 0.82 | 0.84 | 78 | empty |
Interfaces
4 interfaces between chains.
- B–C · 827 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 763 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 194 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 105 Ų buried · 1 hydrogen bond · 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 5TFU · PDBe 5TFU · UniProt P10635
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