Research workbench
Human cytochrome P450 2E1 in complex with omega-imidazolyl-dodecanoic acid
Analyse Human cytochrome P450 2E1 in complex with omega-imidazolyl-dodecanoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LC4
- Type
- protein
- Length
- 919 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 2E1
- EC
- 1.14.13.-
- UniProt
- P05181
- Ligands
- HEM, LC4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 2E1 (EC 1.14.13.-) | protein | 460 | 52% helix, 11% strand | P05181 |
| B | Cytochrome P450 2E1 (EC 1.14.13.-) | protein | 459 | 51% helix, 10% strand | P05181 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- LC4 · 12-(1H-imidazol-1-yl)dodecanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.85 | 0.92 | 62 | HEM, LC4 |
| 2 | 469 | 0.84 | 0.91 | 62 | HEM, LC4 |
| 3 | 228 | 0.78 | 0.91 | 38 | empty |
| 4 | 235 | 0.78 | 0.91 | 40 | empty |
| 5 | 455 | 0.59 | 0.75 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LC4 · Human Cytochrome P450 2E1 in Complex with Omega-Imidazolyl-Dodecanoic Acid · the same entry in another collection · chain A against A, TM-score 1.00
- P05181 · AlphaFold monomer V2.0 prediction for cytochrome P450 2E1 (P05181) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P05181
- Elsewhere: RCSB PDB 3LC4 · PDBe 3LC4 · UniProt P05181
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