MolNFT v1 · #80898 · protein
Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene
3UAS: “Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator 9-ethynylphenanthrene”. X-ray diffraction, 4 ligands (TAM, HEM, 0BV), 8 pockets (best druggability 0.87). MolNFT v1 #80898 on GenesisL1: 3D structure, binding…
- PDB
- 3UAS
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B4
- EC
- 1.14.14.1
- UniProt
- P00178
- Ligands
- TAM, HEM, 0BV, CM5
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 461 | 52% helix, 10% strand | P00178 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 2 copies · chains A
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- 0BV · phenanthren-9-ylacetaldehyde · ligand · chains A
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.87 | 0.94 | 56 | HEM, 0BV |
| 2 | 90 | 0.72 | 0.93 | 16 | empty |
| 3 | 62 | 0.45 | 0.82 | 12 | empty |
| 4 | 118 | 0.42 | 0.76 | 30 | TAM |
| 5 | 73 | 0.37 | 0.78 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3UAS · Cytochrome P450 2B4 covalently bound to the mechanism-based inactivator… · the same entry in another collection · chain A against A, TM-score 1.00
- P00178 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B4 (P00178) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00178
- Elsewhere: RCSB PDB 3UAS · PDBe 3UAS · UniProt P00178
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