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Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor

Analyse Crystal structure of soluble epoxide hydrolase in complex with fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3WK8
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: S0E, MG, PO4
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	Bifunctional epoxide hydrolase 2 (EC 3.3.2.10, 3.1.3.76)	protein	546	47% helix, 14% strand	P34913

Ligands and binding sites

S0E · 6-(trifluoromethyl)-1,3-benzothiazol-2-amine · ligand · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	396	0.78	0.87	29	empty
2	164	0.75	0.92	26	S0E
3	496	0.61	0.75	39	empty
4	185	0.59	0.82	26	PO4

Compared structures

3WK8 · Crystal structure of soluble epoxide hydrolase in complex with fragment inhibitor · 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 3WK8 · PDBe 3WK8 · UniProt P34913

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