Research workbench
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
- 5ALI
- 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
- Q3B, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 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
- Q3B · 1-[3-[5-(7-aminothiazolo[5,4-d]pyrimidin-2-yl)-1-[[(2S)-tetrahydrofuran-2-yl]methyl]imidazol-4-yl]phenyl]-3-(4-methoxyphenyl)urea · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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 | 463 | 0.79 | 0.86 | 37 | Q3B |
| 2 | 172 | 0.74 | 0.90 | 26 | SO4 |
| 3 | 496 | 0.60 | 0.74 | 42 | empty |
| 4 | 179 | 0.54 | 0.79 | 28 | empty |
| 5 | 55 | 0.31 | 0.76 | 15 | empty |
Compared structures
- 5ALI · ligand complex structure of soluble epoxide hydrolase · 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 5ALI · PDBe 5ALI · UniProt P34913
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