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 17 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 16 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 12 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 = 0.048 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
Ligand no: 1; Ligand: AH0 NAG; Similar ligands found: 83
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 NAG GAL 0.532468 0.833333
7 GAL NAG 0.532468 0.833333
8 NGA GAL 0.531646 0.785714
9 NAG A2G 0.525641 0.888889
10 NAG NGA 0.525641 0.888889
11 NAG NAG 0.518519 0.810345
12 NAG NDG 0.518519 0.810345
13 CBS CBS 0.506329 0.888889
14 NDG NAG 0.506329 0.888889
15 NAG GDL 0.506329 0.888889
16 CBS 0.506329 0.888889
17 NOJ NAG NAG NAG 0.488889 0.803279
18 NOJ NAG NAG 0.488889 0.786885
19 GAL NGA A2G 0.488095 0.888889
20 NAG MBG 0.4875 0.836364
21 NDG NAG NAG 0.481928 0.907407
22 NDG NAG NAG NDG 0.481928 0.907407
23 NAG NAG NDG NAG 0.481928 0.907407
24 NAG NAG NDG 0.481928 0.907407
25 NAG NAG NAG NAG NDG 0.481928 0.907407
26 NDG NAG NAG NAG 0.481928 0.907407
27 NAG NAG NAG NAG NAG NAG 0.481928 0.907407
28 NAG NAG NAG NAG NAG 0.481928 0.907407
29 CTO 0.481928 0.907407
30 NAG NAG NAG NDG 0.481928 0.907407
31 NAG NAG NAG NAG NAG NAG NAG NAG 0.481928 0.907407
32 A2G MBG 0.481481 0.836364
33 MBG A2G 0.481481 0.836364
34 NAG NAG NAG 0.477273 0.844828
35 MAN MAN NAG 0.477273 0.803571
36 NAG NAG NAG NAG 0.477273 0.844828
37 NAG MAN BMA 0.476744 0.833333
38 NAG AMU 0.466667 0.890909
39 NAG MUB 0.466667 0.890909
40 FUC GLA A2G 0.465909 0.851852
41 A2G GAL FUC 0.465909 0.851852
42 FUC GAL A2G 0.465909 0.851852
43 NGA GAL FUC 0.465909 0.851852
44 A2G GLA FUC 0.465909 0.851852
45 NGA GAL BGC 0.465116 0.833333
46 NAG GAL BGC 0.460674 0.833333
47 NAG GAL NAG 0.460674 0.888889
48 NAG MAN MAN 0.455556 0.833333
49 2F8 0.452055 0.781818
50 MAG 0.452055 0.781818
51 NAG NM9 0.444444 0.875
52 MLD 0.444444 0.868852
53 FUC BGC GAL NAG 0.443299 0.851852
54 NAG MAN 0.440476 0.87037
55 GYU 0.439024 0.770492
56 NAG MAN MMA 0.438202 0.836364
57 NAG MAN MAN MAN NAG 0.4375 0.888889
58 NGA GLA GAL BGC 0.43617 0.833333
59 DLD 0.430108 0.75
60 FHY 0.428571 0.877193
61 NG1 0.428571 0.698413
62 GN1 0.428571 0.698413
63 LEC NGA 0.427083 0.710145
64 6Y2 0.427083 0.710145
65 BMA Z4Y NAG 0.427083 0.818182
66 BGC FUC GAL FUC A2G 0.424242 0.87037
67 GLC FUC GAL FUC A2G 0.424242 0.87037
68 NGT NAG 0.423913 0.836066
69 3YW 0.419753 0.763636
70 BGA 0.415842 0.786885
71 GAL NAG MAN 0.411111 0.833333
72 NAG BDP NAG BDP NAG BDP NAG 0.41 0.890909
73 3PV 0.41 0.857143
74 GAL NAG GAL 0.408602 0.803571
75 A2G GAL BGC FUC 0.405941 0.851852
76 A2G GAL NAG FUC 0.405941 0.907407
77 FUC GAL NAG A2G 0.405941 0.907407
78 TNR 0.404762 0.789474
79 NAG A2G GAL 0.404255 0.888889
80 NAG NDG BMA 0.404255 0.827586
81 NAG NAG BMA 0.404255 0.827586
82 MMA MAN NAG MAN NAG NAG 0.4 0.890909
83 NAG AMU NAG AMV 0.4 0.875
Ligand no: 2; Ligand: NAG AH0; Similar ligands found: 76
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 NAG MUB 0.611765 0.925926
6 NAG AMU 0.611765 0.925926
7 Z4S NAG NAG 0.561798 0.981481
8 NAG AMU NAG AMV 0.55914 0.909091
9 MLD 0.532787 0.868852
10 NAG NM9 0.5 0.875
11 NGA GAL 0.5 0.785714
12 NAG NDG 0.488372 0.810345
13 NAG NAG 0.488372 0.810345
14 MAN MAN NAG 0.483516 0.803571
15 NAG GAL 0.481928 0.833333
16 GAL NAG 0.481928 0.833333
17 NAG NGA 0.47619 0.888889
18 NAG A2G 0.47619 0.888889
19 MBG A2G 0.470588 0.836364
20 A2G MBG 0.470588 0.836364
21 NAG MAN BMA 0.466667 0.833333
22 NOJ NAG NAG 0.463158 0.816667
23 NOJ NAG NAG NAG 0.463158 0.833333
24 NAG MBG 0.458824 0.836364
25 CBS CBS 0.458824 0.888889
26 NAG GDL 0.458824 0.888889
27 CBS 0.458824 0.888889
28 NDG NAG 0.458824 0.888889
29 NAG NAG NAG NAG 0.451613 0.844828
30 NAG NAG NAG 0.451613 0.844828
31 NAG MAN MMA 0.445652 0.836364
32 NAG AMU ALA DGL 0.445455 0.862069
33 GAL NGA A2G 0.444444 0.888889
34 NAG AH0 ALA DGL API DAL DAL 0.440298 0.870968
35 NGA GAL BGC 0.43956 0.833333
36 NAG NAG NDG NAG 0.438202 0.907407
37 NAG NAG NAG NAG NDG 0.438202 0.907407
38 NAG NAG NAG NAG NAG NAG 0.438202 0.907407
39 NAG NAG NAG NAG NAG NAG NAG NAG 0.438202 0.907407
40 NAG NAG NAG NAG NAG 0.438202 0.907407
41 NAG NAG NAG NDG 0.438202 0.907407
42 NDG NAG NAG 0.438202 0.907407
43 NDG NAG NAG NAG 0.438202 0.907407
44 NDG NAG NAG NDG 0.438202 0.907407
45 CTO 0.438202 0.907407
46 NAG NAG NDG 0.438202 0.907407
47 AH0 0.435294 0.833333
48 NAG MAN MAN 0.431579 0.833333
49 NAG MU2 0.428571 0.847458
50 FUC GAL A2G 0.425532 0.851852
51 FUC GLA A2G 0.425532 0.851852
52 A2G GLA FUC 0.425532 0.851852
53 A2G GAL FUC 0.425532 0.851852
54 NGA GAL FUC 0.425532 0.851852
55 MAG 0.423077 0.781818
56 2F8 0.423077 0.781818
57 NAG GAL BGC 0.421053 0.833333
58 6Y2 0.42 0.735294
59 LEC NGA 0.42 0.735294
60 89A 0.419355 0.875
61 NAG BDP NAG BDP NAG BDP NAG 0.417476 0.925926
62 NAG MAN MAN MAN NAG 0.415842 0.888889
63 MA8 0.41573 0.745763
64 NAG MAN 0.41573 0.87037
65 DLD 0.408163 0.777778
66 FHY 0.407767 0.877193
67 NAG GAL NAG 0.40625 0.888889
68 BMA Z4Y NAG 0.405941 0.818182
69 BGC FUC GAL FUC A2G 0.403846 0.87037
70 GLC FUC GAL FUC A2G 0.403846 0.87037
71 GN1 0.402439 0.698413
72 NG1 0.402439 0.698413
73 NGT NAG 0.402062 0.836066
74 THR NGA GAL NAG 0.401869 0.909091
75 A2G GAL BGC FUC 0.4 0.851852
76 NGA GLA GAL BGC 0.4 0.833333
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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