Research workbench
Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor
Analyse Crystal structure of soluble epoxide hydrolase in complex with fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WK5
- Type
- protein
- Length
- 546 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.77
- Source
- Homo sapiens
- Molecule
- Bifunctional epoxide hydrolase 2
- EC
- 3.3.2.10, 3.1.3.76
- UniProt
- P34913
- Ligands
- S0C, MG, PO4
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.77 · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional epoxide hydrolase 2 (EC 3.3.2.10, 3.1.3.76) | protein | 546 | 47% helix, 15% strand | P34913 |
Ligands and binding sites
- S0C · 2-cyclopentyl-N-(1,3-thiazol-2-yl)acetamide · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.83 | 0.87 | 54 | S0C |
| 2 | 214 | 0.63 | 0.82 | 34 | MG, PO4 |
| 3 | 433 | 0.60 | 0.75 | 34 | empty |
Compared structures
- 3WK5 · Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P34913 · AlphaFold monomer V2.0 prediction for bifunctional epoxide hydrolase 2 (P34913) · a predicted model of the same protein · chain A against A, TM-score 0.71
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 3WK5 · PDBe 3WK5 · UniProt P34913
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