MolNFT v1 · #113606 · protein

Ligand complex structure of soluble epoxide hydrolase

5AKK · Bifunctional epoxide hydrolase 2: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (1P8, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #113606 on GenesisL1: 3D structure, binding sites and…

PDB: 5AKK
Type: protein
Length: 541 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: 1P8, SO4
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 46% 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	541	46% helix, 14% strand	P34913

Ligands and binding sites

1P8 · 6-bromo-1,3-dihydro-2H-indol-2-one · ligand · 2 copies · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 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	433	0.80	0.87	32	SO4, 1P8
2	231	0.75	0.89	32	empty
3	549	0.61	0.74	39	empty
4	197	0.61	0.82	35	empty
5	59	0.32	0.76	15	empty

Compared structures

5AKK · 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 5AKK · PDBe 5AKK · UniProt P34913

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