Receptor
PDB id Resolution Class Description Source Keywords
3NVD 1.84 Å EC: 3.2.1.52 STRUCTURE OF YBBD IN COMPLEX WITH PUGNAC BACILLUS SUBTILIS BETA-N-HEXOSAMINIDASE BACILLUS SUBTILIS TIM BARREL GLYCOSHYDROLASE LIPOPROTEIN MEMBRANE PALMITATE
Ref.: STRUCTURAL AND KINETIC ANALYSIS OF BACILLUS SUBTILI N-ACETYLGLUCOSAMINIDASE REVEALS A UNIQUE ASP-HIS DY MECHANISM J.BIOL.CHEM. V. 285 35675 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:644;
A:645;
B:644;
B:645;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
NA A:643;
B:643;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
OAN A:646;
B:646;
 Valid;
Valid;
 none;
none;
 submit data
353.327 C15 H19 N3 O7 CC(=O...
PG4 A:647;
 Invalid;
 none;
 submit data
194.226 C8 H18 O5 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NVD 1.84 Å EC: 3.2.1.52 STRUCTURE OF YBBD IN COMPLEX WITH PUGNAC BACILLUS SUBTILIS BETA-N-HEXOSAMINIDASE BACILLUS SUBTILIS TIM BARREL GLYCOSHYDROLASE LIPOPROTEIN MEMBRANE PALMITATE
Ref.: STRUCTURAL AND KINETIC ANALYSIS OF BACILLUS SUBTILI N-ACETYLGLUCOSAMINIDASE REVEALS A UNIQUE ASP-HIS DY MECHANISM J.BIOL.CHEM. V. 285 35675 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4GYK - MUB NAG n/a n/a
2 4GYJ - MUB NAG n/a n/a
3 3NVD - OAN C15 H19 N3 O7 CC(=O)N[C@....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 4GYK - MUB NAG n/a n/a
2 4GYJ - MUB NAG n/a n/a
3 3NVD - OAN C15 H19 N3 O7 CC(=O)N[C@....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 4GYK - MUB NAG n/a n/a
2 4GYJ - MUB NAG n/a n/a
3 3NVD - OAN C15 H19 N3 O7 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: OAN; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 OAN 1 1
2 OGN 1 1
3 8M7 0.76 0.951613
4 NP6 0.76 0.921875
5 VPU 0.730769 0.893939
6 GDL PHJ NAG 0.622222 0.967213
7 5G0 GAL 0.56044 0.838235
8 GYZ 0.5 0.864407
9 LOG 0.492754 0.833333
Similar Ligands (3D)
Ligand no: 1; Ligand: OAN; Similar ligands found: 5
No: Ligand Similarity coefficient
1 GDV 0.9250
2 V0N 0.9025
3 LEC 0.9022
4 FVQ 0.8584
5 IDE 0.8583
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NVD; 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: 3nvd.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3NVD; 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: 2) in the query (biounit: 3nvd.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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