Receptor
PDB id Resolution Class Description Source Keywords
4GVI 1.55 Å EC: 3.2.1.52 CRYSTAL STRUCTURE OF MUTANT (D248N) SALMONELLA TYPHIMURIUM F GLYCOSIDE HYDROLASE (NAGZ) IN COMPLEX WITH GLCNAC-1,6-ANHMU SALMONELLA ENTERICA SUBSP. ENTERICA SETYPHIMURIUM TIM-BARREL HYDROLASE
Ref.: ACTIVE SITE PLASTICITY WITHIN THE GLYCOSIDE HYDROLA UNDERLIES A DYNAMIC MECHANISM OF SUBSTRATE DISTORTI CHEM.BIOL. V. 19 1471 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AH0 NAG B:401;
 Valid;
 none;
 submit data
434.442 n/a O=C(N...
MES B:403;
 Invalid;
 none;
 submit data
195.237 C6 H13 N O4 S C1COC...
NAG AH0 A:401;
 Valid;
 none;
 submit data
477.443 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GVF 1.35 Å EC: 3.2.1.52 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM FAMILY 3 GLYCOSI HYDROLASE (NAGZ) BOUND TO GLCNAC SALMONELLA ENTERICA SUBSP. ENTERICA SETYPHIMURIUM TIM-BARREL HYDROLASE
Ref.: ACTIVE SITE PLASTICITY WITHIN THE GLYCOSIDE HYDROLA UNDERLIES A DYNAMIC MECHANISM OF SUBSTRATE DISTORTI CHEM.BIOL. V. 19 1471 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
2 4GVI - NAG AH0 n/a n/a
3 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
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 4GVF - NAG C8 H15 N O6 CC(=O)N[C@....
2 4GVI - NAG AH0 n/a n/a
3 4HZM Ki = 23.2 uM 1BW C10 H20 N2 O4 CCCC(=O)N[....
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: AH0 NAG; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 AH0 NAG 1 1
2 NAG AH0 0.691358 0.963636
3 3QL 0.657895 0.962963
4 ALA NAG AH0 DAL 0.602151 0.946429
5 Z4S NAG NAG 0.595238 0.981481
6 MAN NAG 0.539474 0.833333
7 GAL NGA 0.531646 0.785714
8 A2G NAG 0.525641 0.888889
9 GDL NAG 0.506329 0.888889
10 NDG NAG 0.493827 0.907407
11 NAG NOJ NAG 0.488889 0.786885
12 NAG NOJ NAG NAG 0.488889 0.803279
13 GAL NGA A2G 0.488095 0.888889
14 MBG NAG 0.4875 0.836364
15 NAG NAG NAG NAG NAG 0.481928 0.907407
16 NDG NAG NAG NAG NAG 0.481928 0.907407
17 NAG NAG NAG NAG NAG NAG NAG NAG 0.481928 0.907407
18 NAG NAG NAG NAG NAG NAG 0.481928 0.907407
19 MBG A2G 0.481481 0.836364
20 NAG NAG NAG 0.477273 0.844828
21 NAG NAG NAG NAG 0.477273 0.844828
22 NAG NAG NAG NAG NAG NAG NAG 0.477273 0.844828
23 MAN MAN NAG 0.477273 0.803571
24 AMU NAG 0.466667 0.890909
25 GAL FUC A2G 0.465909 0.851852
26 BMA MAN NAG 0.465909 0.833333
27 BGC GAL NGA 0.465116 0.833333
28 NAG GAL NAG 0.460674 0.888889
29 BGC GAL NAG 0.460674 0.833333
30 2F8 0.452055 0.781818
31 MAG 0.452055 0.781818
32 NAG NGO 0.449438 0.877193
33 MLD 0.444444 0.868852
34 NM9 NAG 0.444444 0.875
35 BGC FUC GAL NAG 0.443299 0.851852
36 NAG AH0 ALA DGL API DAL DAL 0.442748 0.828125
37 GYU 0.439024 0.770492
38 MMA MAN NAG 0.438202 0.836364
39 MAN MAN MAN NAG NAG 0.4375 0.888889
40 NAG GAL GLC NAG GLC RAM 0.4375 0.888889
41 BGC GAL GLA NGA 0.43617 0.833333
42 Z3Q NGA 0.434783 0.738462
43 GN1 0.428571 0.698413
44 FHY 0.428571 0.877193
45 NG1 0.428571 0.698413
46 BMA Z4Y NAG 0.427083 0.818182
47 LEC NGA 0.427083 0.710145
48 6Y2 0.427083 0.710145
49 HSH A2G FUC 0.424242 0.786885
50 BGC FUC GAL FUC A2G 0.424242 0.87037
51 NGT NAG 0.423913 0.836066
52 SER A2G 0.421687 0.775862
53 3YW 0.419753 0.763636
54 GAL NAG 0.411765 0.833333
55 MAN NAG GAL 0.411111 0.833333
56 NAG BDP NAG BDP NAG BDP NAG 0.41 0.890909
57 GYP GZL NAG 0.41 0.857143
58 GAL NAG GAL 0.406593 0.833333
59 BGC GAL FUC A2G 0.405941 0.851852
60 TNR 0.404762 0.789474
61 A2G GAL NAG 0.404255 0.888889
62 NAG NAG BMA 0.404255 0.827586
63 NAG NAG BMA MAN NAG 0.401961 0.907407
64 AMV NAG AMU NAG 0.4 0.875
65 MMA MAN NAG MAN NAG NAG 0.4 0.890909
Ligand no: 2; Ligand: NAG AH0; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG AH0 1 1
2 ALA NAG AH0 DAL 0.790698 0.981818
3 AH0 NAG 0.691358 0.963636
4 3QL 0.617284 0.962963
5 AMU NAG 0.611765 0.925926
6 Z4S NAG NAG 0.561798 0.981481
7 AMV NAG AMU NAG 0.55914 0.909091
8 NAG AH0 ALA DGL API DAL DAL 0.539683 0.857143
9 MLD 0.532787 0.868852
10 MAN NAG 0.506173 0.833333
11 GAL NGA 0.5 0.785714
12 NM9 NAG 0.5 0.875
13 MAN MAN NAG 0.483516 0.803571
14 A2G NAG 0.47619 0.888889
15 MBG A2G 0.470588 0.836364
16 NAG NOJ NAG 0.463158 0.816667
17 NAG NOJ NAG NAG 0.463158 0.833333
18 MBG NAG 0.458824 0.836364
19 GDL NAG 0.458824 0.888889
20 NAG NAG NAG NAG 0.451613 0.844828
21 NAG NAG NAG 0.451613 0.844828
22 NAG NAG NAG NAG NAG NAG NAG 0.451613 0.844828
23 NDG NAG 0.448276 0.907407
24 MMA MAN NAG 0.445652 0.836364
25 AMU ALA NAG DGL 0.445455 0.862069
26 GAL NGA A2G 0.444444 0.888889
27 BMA MAN NAG 0.44086 0.833333
28 BGC GAL NGA 0.43956 0.833333
29 NAG NAG NAG NAG NAG NAG NAG NAG 0.438202 0.907407
30 NAG NAG NAG NAG NAG NAG 0.438202 0.907407
31 NAG NAG NAG NAG NAG 0.438202 0.907407
32 NDG NAG NAG NAG NAG 0.438202 0.907407
33 MUB ALA NAG DGN 0.4375 0.847458
34 MUB ALA NAG GLN 0.4375 0.862069
35 AH0 0.435294 0.833333
36 SER A2G 0.430233 0.807018
37 MUB ALA NAG ZGL 0.428571 0.847458
38 NAG NGO 0.425532 0.910714
39 GAL FUC A2G 0.425532 0.851852
40 MAG 0.423077 0.781818
41 2F8 0.423077 0.781818
42 BGC GAL NAG 0.421053 0.833333
43 6Y2 0.42 0.735294
44 LEC NGA 0.42 0.735294
45 89A 0.419355 0.875
46 NAG BDP NAG BDP NAG BDP NAG 0.417476 0.925926
47 MAN MAN MAN NAG NAG 0.415842 0.888889
48 MA8 0.41573 0.745763
49 FHY 0.407767 0.877193
50 NAG GAL NAG 0.40625 0.888889
51 BMA Z4Y NAG 0.405941 0.818182
52 BGC FUC GAL FUC A2G 0.403846 0.87037
53 NG1 0.402439 0.698413
54 GN1 0.402439 0.698413
55 NGT NAG 0.402062 0.836066
56 A2G THR GAL NAG 0.401869 0.909091
57 BGC GAL FUC A2G 0.4 0.851852
58 BGC GAL GLA NGA 0.4 0.833333
Similar Ligands (3D)
Ligand no: 1; Ligand: AH0 NAG; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: NAG AH0; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GVF; Ligand: NDG; 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: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4GVF; Ligand: NAG; 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: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4GVF; Ligand: NAG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4GVF; Ligand: NDG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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