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ligand complex structure of soluble epoxide hydrolase
Analyse ligand complex structure of soluble epoxide hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ALL
- Type
- protein
- Length
- 546 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- HOMO SAPIENS
- Molecule
- Soluble epoxide hydrolase
- UniProt
- P34913
- Ligands
- II6, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble epoxide hydrolase | protein | 546 | 46% helix, 14% strand | P34913 |
Ligands and binding sites
- II6 · [(1R,3S,5R)-3-(aminomethyl)-5-methyl-cyclohexyl]methanol · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.78 | 0.86 | 31 | SO4 |
| 2 | 227 | 0.76 | 0.89 | 26 | II6 |
| 3 | 266 | 0.66 | 0.82 | 36 | empty |
| 4 | 461 | 0.59 | 0.74 | 40 | empty |
| 5 | 66 | 0.34 | 0.76 | 15 | 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 P34913
- Elsewhere: RCSB PDB 5ALL · PDBe 5ALL · UniProt P34913
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