MolNFT v1 · #51966 · protein
CYP2C8DH complexed with troglitazone
2VN0 · Cytochrome P450 2C8: “CYP2C8DH complexed with troglitazone”. X-ray diffraction, 3 ligands (HEM, TDZ, PLM), 3 pockets (best druggability 0.87). MolNFT v1 #51966 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2VN0
- Type
- protein
- Length
- 464 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2C8
- EC
- 1.14.14.1
- UniProt
- P10632
- Ligands
- HEM, TDZ, PLM
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2C8 (EC 1.14.14.1) | protein | 464 | 53% helix, 10% strand | P10632 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- TDZ · (5R)-5-(4-{[(2R)-6-hydroxy-2,5,7,8-tetramethyl-3,4-dihydro-2H-chromen-2-yl]methoxy}benzyl)-1,3-thiazolidine-2,4-dione · ligand · chains A
- PLM · Palmitic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.87 | 0.88 | 111 | HEM, TDZ |
| 2 | 112 | 0.65 | 0.88 | 16 | PLM |
| 3 | 80 | 0.35 | 0.76 | 17 | empty |
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 P10632
- Elsewhere: RCSB PDB 2VN0 · PDBe 2VN0 · UniProt P10632
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