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
- 3WKD
- Type
- protein
- Length
- 546 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional epoxide hydrolase 2
- EC
- 3.3.2.10, 3.1.3.76
- UniProt
- P34913
- Ligands
- S0K, MG, PO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 14% 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 | 46% helix, 14% strand | P34913 |
Ligands and binding sites
- S0K · N-[2-(morpholin-4-yl)phenyl]thiophene-3-carboxamide · 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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.80 | 0.86 | 37 | S0K |
| 2 | 180 | 0.72 | 0.89 | 28 | empty |
| 3 | 250 | 0.66 | 0.83 | 35 | MG, PO4 |
| 4 | 442 | 0.60 | 0.75 | 36 | empty |
| 5 | 56 | 0.27 | 0.74 | 10 | empty |
Compared structures
- 3WKD · 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
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 3WKD · PDBe 3WKD · UniProt P34913
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