Receptor
PDB id Resolution Class Description Source Keywords
3GSM 2.4 Å EC: 3.2.1.52 VIBRIO CHOLERAE FAMILY 3 GLYCOSIDE HYDROLASE (NAGZ) BOUND TO VALERYL-PUGNAC VIBRIO CHOLERAE GLYCOSIDE HYDROLASES CELL CYCLE CELL DIVISION CELL SHAPEWALL BIOGENESIS/DEGRADATION GLYCOSIDASE HYDROLASE PEPTIDSYNTHESIS
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:343;
A:344;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
VPU A:341;
 Valid;
 none;
 submit data
395.407 C18 H25 N3 O7 CCCCC...
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: VPU; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 VPU 1 1
2 NP6 0.855263 0.969697
3 OAN 0.730769 0.893939
4 OGN 0.730769 0.893939
5 8M7 0.719512 0.910448
6 5G0 GAL 0.51 0.808219
7 GDL PHJ NAG 0.490385 0.867647
8 GYZ 0.482353 0.772727
Similar Ligands (3D)
Ligand no: 1; Ligand: VPU; Similar ligands found: 30
No: Ligand Similarity coefficient
1 BGN 0.9685
2 1BW 0.9457
3 8MP 0.9173
4 YX1 0.9163
5 STZ 0.9151
6 NAG 0.8950
7 NDG 0.8935
8 H4B 0.8901
9 ALJ 0.8886
10 GDL 0.8832
11 SJK 0.8825
12 H6Q 0.8816
13 DL6 0.8792
14 JYE 0.8780
15 3L1 0.8745
16 BNX 0.8737
17 DBT 0.8729
18 GZV 0.8690
19 CG 0.8690
20 X0T 0.8684
21 H6Z 0.8661
22 UQ1 0.8648
23 F5C 0.8646
24 16G 0.8644
25 MQG 0.8611
26 EEK 0.8596
27 3JN 0.8589
28 4QY 0.8582
29 5F1 0.8568
30 CDY 0.8534
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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