MolNFT v1 · #113643 · protein

Ligand complex structure of soluble epoxide hydrolase

5ALL: “Ligand complex structure of soluble epoxide hydrolase”. X-ray diffraction, 2 ligands (II6, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #113643 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ALL
Type: protein
Length: 546 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble epoxide hydrolase
UniProt: P34913
Ligands: II6, SO4
Pockets: 6 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Soluble epoxide hydrolase	protein	546	46% helix, 14% strand	P34913

Ligands and binding sites

II6 · [(1R,3S,5R)-3-(aminomethyl)-5-methyl-cyclohexyl]methanol · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
DMS · Dimethyl sulfoxide · additive · 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	407	0.78	0.86	31	SO4
2	227	0.76	0.89	26	II6
3	266	0.66	0.82	36	empty
4	461	0.59	0.74	40	empty
5	66	0.34	0.76	15	empty

Compared structures

5ALL · 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 5ALL · PDBe 5ALL · UniProt P34913

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