MolNFT v1 · #113600 · protein

Ligand complex structure of soluble epoxide hydrolase

5AKE · Bifunctional epoxide hydrolase 2: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (6N0, SO4), 3 pockets (best druggability 0.85). MolNFT v1 #113600 on GenesisL1: 3D structure, binding sites and…

PDB: 5AKE
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: 6N0, SO4
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 45% 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	45% helix, 14% strand	P34913

Ligands and binding sites

6N0 · N-(5,5-dioxodibenzothiophen-2-yl)-4,4-difluoro-piperidine-1-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · chains A
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · chains A

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.85	0.88	55	SO4, 6N0
2	427	0.57	0.74	42	empty
3	138	0.54	0.81	27	empty

Compared structures

5AKE · 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 5AKE · PDBe 5AKE · UniProt P34913

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