MolNFT v1 · #64516 · protein
Triple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole
3G5N: “Triple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the inhibitor…”. X-ray diffraction, 3 ligands (PB2, HEM, CM5), 20 pockets (best druggability 0.89). MolNFT v1 #64516 on GenesisL1: 3D structure…
- PDB
- 3G5N
- Type
- protein
- Length
- 1,810 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2B4
- EC
- 1.14.14.1
- UniProt
- P00178
- Ligands
- PB2, HEM, CM5
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 456 | 52% helix, 10% strand | P00178 |
| B | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 451 | 52% helix, 11% strand | P00178 |
| C | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 452 | 52% helix, 12% strand | P00178 |
| D | Cytochrome P450 2B4 (EC 1.14.14.1) | protein | 451 | 52% helix, 12% strand | P00178 |
Ligands and binding sites
- PB2 · 1-(biphenyl-4-ylmethyl)-1H-imidazole · ligand · 12 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- CM5 · 5-cyclohexyl-1-pentyl-beta-D-maltoside · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.89 | 0.93 | 101 | HEM, PB2 |
| 2 | 638 | 0.89 | 0.93 | 96 | HEM, PB2 |
| 3 | 587 | 0.88 | 0.93 | 94 | PB2, HEM |
| 4 | 546 | 0.88 | 0.93 | 88 | HEM, PB2 |
| 5 | 629 | 0.75 | 0.81 | 58 | CM5 |
Interfaces
6 interfaces between chains.
- A–B · 4277 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 4182 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 553 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 532 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3G5N · Triple ligand occupancy crystal structure of cytochrome P450 2B4 in complex with the… · the same entry in another collection · chain D against D, TM-score 1.00
- P00178 · AlphaFold monomer V2.0 prediction for cytochrome P450 2B4 (P00178) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 3G5N · PDBe 3G5N · UniProt P00178
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