MolNFT v1 · #5506 · protein
Crystal structure of murine soluble epoxide hydrolase complexed with cdu inhibitor
1EK2: “Crystal structure of murine soluble epoxide hydrolase complexed with cdu inhibitor”. X-ray diffraction, 1 ligand (CDU), 11 pockets (best druggability 0.85). MolNFT v1 #5506 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1EK2
- Type
- protein
- Length
- 1,028 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxide hydrolase
- EC
- 3.3.2.3
- UniProt
- P34914
- Ligands
- CDU
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxide hydrolase (EC 3.3.2.3) | protein | 487 | 39% helix, 13% strand | P34914 |
| B | Epoxide hydrolase (EC 3.3.2.3) | protein | 541 | 40% helix, 12% strand | P34914 |
Ligands and binding sites
- CDU · N-cyclohexyl-N'-decylurea · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.85 | 0.89 | 61 | CDU |
| 2 | 608 | 0.84 | 0.89 | 62 | CDU |
| 3 | 1059 | 0.77 | 0.79 | 115 | empty |
| 4 | 98 | 0.74 | 0.95 | 34 | empty |
| 5 | 404 | 0.68 | 0.81 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2360 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 1EK2 · Crystal structure of murine soluble epoxide hydrolase complexed with cdu inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P34914 · AlphaFold monomer V2.0 prediction for bifunctional epoxide hydrolase 2 (P34914) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P34914
- Elsewhere: RCSB PDB 1EK2 · PDBe 1EK2 · UniProt P34914
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