MolNFT v1 · #113662 · protein

Ligand complex structure of soluble epoxide hydrolase

5AM4 · Bifunctional epoxide hydrolase 2: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (MVJ, SO4), 5 pockets (best druggability 0.80). MolNFT v1 #113662 on GenesisL1: 3D structure, binding sites and…

PDB: 5AM4
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: MVJ, SO4
Pockets: 5 · best druggability 0.80

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

MVJ · 5-cyclohexylspiro[1H-indole-3,4'-oxane]-2-one · ligand · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A
DMS · Dimethyl sulfoxide · additive · 7 copies · chains A

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

Pockets

5 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	388	0.80	0.88	35	SO4
2	200	0.78	0.92	28	MVJ
3	263	0.64	0.81	36	empty
4	503	0.60	0.74	46	DMS
5	52	0.30	0.76	15	empty

Compared structures

5AM4 · 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 5AM4 · PDBe 5AM4 · UniProt P34913

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