MolNFT v1 · #113661 · protein
Ligand complex structure of soluble epoxide hydrolase
5AM3 · Bifunctional epoxide hydrolase 2: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (AUB, SO4), 4 pockets (best druggability 0.83). MolNFT v1 #113661 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5AM3
- 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
- AUB, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% 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 | 47% helix, 14% strand | P34913 |
Ligands and binding sites
- AUB · 4-[(trans-4-{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbamoyl]amino}cyclohexyl)oxy]benzoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- GOL · Glycerol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.83 | 0.87 | 64 | AUB |
| 2 | 240 | 0.67 | 0.84 | 33 | empty |
| 3 | 543 | 0.61 | 0.74 | 44 | PEG |
| 4 | 51 | 0.28 | 0.75 | 14 | empty |
Compared structures
- 5AM3 · 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 5AM3 · PDBe 5AM3 · UniProt P34913
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