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Crystal structure of human soluble epoxide hydrolase complexed with 1- (1-propanoylpiperidin-4-yl)-3-[4-(TRIFLUOROMETHOXY)PHENYL]UREA
Analyse Crystal structure of human soluble epoxide hydrolase complexed with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OD0
- Type
- protein
- Length
- 547 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
- 2RV, MG, PO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 48% 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 | 547 | 48% helix, 14% strand | P34913 |
Ligands and binding sites
- 2RV · 1-(1-propanoylpiperidin-4-yl)-3-[4-(trifluoromethoxy)phenyl]urea · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.83 | 0.88 | 54 | 2RV |
| 2 | 181 | 0.62 | 0.83 | 31 | PO4, MG |
| 3 | 431 | 0.59 | 0.74 | 44 | empty |
| 4 | 61 | 0.32 | 0.76 | 16 | empty |
| 5 | 54 | 0.27 | 0.74 | 15 | empty |
Compared structures
- 4OD0 · Crystal structure of human soluble epoxide hydrolase complexed with… · 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 4OD0 · PDBe 4OD0 · UniProt P34913
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