MolNFT v1 · #113619 · protein
Ligand complex structure of soluble epoxide hydrolase
5AKX: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (8NY, SO4), 4 pockets (best druggability 0.78). MolNFT v1 #113619 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5AKX
- Type
- protein
- Length
- 546 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble epoxide hydrolase
- UniProt
- P34913
- Ligands
- 8NY, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble epoxide hydrolase | protein | 546 | 47% helix, 14% strand | P34913 |
Ligands and binding sites
- 8NY · 5-iodanyl-1H-indazole · ligand · chains A
- SO4 · Sulfate ion · ion · 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.78 | 0.86 | 29 | DMS |
| 2 | 313 | 0.73 | 0.85 | 40 | empty |
| 3 | 194 | 0.72 | 0.88 | 28 | 8NY |
| 4 | 456 | 0.59 | 0.74 | 36 | empty |
Compared structures
- 5AKX · 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 5AKX · PDBe 5AKX · UniProt P34913
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