Receptor
PDB id Resolution Class Description Source Keywords
3GS6 2.3 Å EC: 3.2.1.52 VIBRIO CHOLEREA FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ)IN COMPLE BUTYRYL-PUGNAC VIBRIO CHOLERAE GLYCOSIDE HYDROLASE FAMILY 3 CELL CYCLE CELL DIVISION CELCELL WALL BIOGENESIS/DEGRADATION GLYCOSIDASE HYDROLASE PEPTIDOGLYCAN SYNTHESIS
Ref.: INSIGHT INTO A STRATEGY FOR ATTENUATING AMPC-MEDIAT BETA-LACTAM RESISTANCE: STRUCTURAL BASIS FOR SELECT INHIBITION OF THE GLYCOSIDE HYDROLASE NAGZ. PROTEIN SCI. V. 18 1541 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:342;
A:343;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
NP6 A:341;
 Valid;
 none;
 submit data
381.38 C17 H23 N3 O7 CCCC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OXN 1.7 Å EC: 3.2.1.52 VIBRIO CHOLERAE FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) IN COMPL PUGNAC VIBRIO CHOLERAE TIM-BARREL HYDROLASE
Ref.: SMALL MOLECULE INHIBITORS OF A GLYCOSIDE HYDROLASE INDUCIBLE AMPC-MEDIATED BETA-LACTAM RESISTANCE. J.BIOL.CHEM. V. 282 21382 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3GSM - VPU C18 H25 N3 O7 CCCCC(=O)N....
2 2OXN Ki = 0.036 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
3 3GS6 - NP6 C17 H23 N3 O7 CCCC(=O)N[....
4 1Y65 - NAG C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3GSM - VPU C18 H25 N3 O7 CCCCC(=O)N....
2 2OXN Ki = 0.036 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
3 3GS6 - NP6 C17 H23 N3 O7 CCCC(=O)N[....
4 1Y65 - NAG C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 5UTQ Ki = 0.05 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
2 5UTP Ki = 3 uM 8M7 C19 H27 N3 O7 CCC(CC)C(=....
3 4MSS Ki = 3.6 uM 2CZ C8 H16 N2 O4 CC(=O)N[C@....
4 5UTR Kd = 7 uM 8MP C10 H20 N2 O4 CCCC(=O)N[....
5 3GSM - VPU C18 H25 N3 O7 CCCCC(=O)N....
6 2OXN Ki = 0.036 uM OAN C15 H19 N3 O7 CC(=O)N[C@....
7 3GS6 - NP6 C17 H23 N3 O7 CCCC(=O)N[....
8 1Y65 - NAG C8 H15 N O6 CC(=O)N[C@....
9 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
10 4GVI - NAG AH0 n/a n/a
11 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
12 5G3R - NAG C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NP6; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 NP6 1 1
2 VPU 0.855263 0.969697
3 OAN 0.76 0.921875
4 OGN 0.76 0.921875
5 8M7 0.746835 0.909091
6 5G0 GAL 0.525773 0.830986
7 GDL PHJ NAG 0.504951 0.893939
8 GYZ 0.481928 0.796875
Similar Ligands (3D)
Ligand no: 1; Ligand: NP6; Similar ligands found: 1
No: Ligand Similarity coefficient
1 GDV 0.8814
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2OXN; Ligand: OAN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2oxn.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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