MolNFT v1 · #75003 · protein
Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole inhibitor
3PDC · Epoxide hydrolase 2: “Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a benzoxazole…”. X-ray diffraction, 1 ligand (ZYI), 3 pockets (best druggability 0.83). MolNFT v1 #75003 on GenesisL1: 3D…
- PDB
- 3PDC
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxide hydrolase 2
- EC
- 3.3.2.10
- UniProt
- P34913
- Ligands
- ZYI
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Epoxide hydrolase 2 (EC 3.3.2.10) | protein | 323 | 41% helix, 15% strand | P34913 |
Ligands and binding sites
- ZYI · N-(5-chloro-1,3-benzoxazol-2-yl)-2-cyclopentylacetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.83 | 0.87 | 52 | ZYI |
| 2 | 406 | 0.77 | 0.86 | 29 | ZYI |
| 3 | 226 | 0.75 | 0.89 | 27 | ZYI |
Compared structures
- 3PDC · Crystal structure of hydrolase domain of human soluble epoxide hydrolase complexed with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P34913 · AlphaFold monomer V2.0 prediction for bifunctional epoxide hydrolase 2 (P34913) · a predicted model of the same protein · 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 3PDC · PDBe 3PDC · UniProt P34913
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