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 0.583333 0.946429
5 MAN NAG 0.539474 0.833333
6 NAG GAL 0.532468 0.833333
7 NGA GAL 0.532468 0.833333
8 GAL NAG 0.532468 0.833333
9 NAG NGA 0.525641 0.888889
10 NAG A2G 0.525641 0.888889
11 NAG NAG 0.518519 0.810345
12 CBS CBS 0.506329 0.888889
13 NAG GDL 0.506329 0.888889
14 CBS 0.506329 0.888889
15 NAG NDG 0.506329 0.888889
16 NDG NAG 0.493827 0.907407
17 NAG MBG 0.4875 0.836364
18 CTO 0.481928 0.907407
19 NAG NAG NAG 0.481928 0.907407
20 NAG NAG NAG NAG NDG NAG 0.481928 0.907407
21 NAG NAG NAG NAG 0.481928 0.907407
22 NAG NAG NAG NAG NAG NAG NAG NAG 0.481928 0.907407
23 NDG NAG NAG 0.481928 0.907407
24 NAG NAG NAG NDG 0.481928 0.907407
25 NDG NAG NAG NDG NAG 0.481928 0.907407
26 NAG NAG NDG 0.481928 0.907407
27 NAG NAG NAG NAG NDG 0.481928 0.907407
28 NDG NAG NAG NAG 0.481928 0.907407
29 NAG NAG NAG NAG NAG 0.481928 0.907407
30 NDG NAG NAG NDG 0.481928 0.907407
31 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 MAN MAN NAG 0.477273 0.803571
35 NAG AMU 0.466667 0.890909
36 NAG MUB 0.466667 0.890909
37 FUC GAL A2G 0.465909 0.851852
38 NGA GAL FUC 0.465909 0.851852
39 FUC GL0 A2G 0.465909 0.851852
40 FUC GLA A2G 0.465909 0.851852
41 A2G GAL FUC 0.465909 0.851852
42 A2G GLA FUC 0.465909 0.851852
43 NGA GAL BGC 0.465116 0.833333
44 NAG GAL BGC 0.460674 0.833333
45 NAG GAL NAG 0.460674 0.888889
46 NAG NGO 0.45977 0.892857
47 NAG MAN MAN 0.455556 0.833333
48 NAG MAN BMA 0.455556 0.833333
49 NAG NAG NAG NAG NAG NAG NAG 0.452632 0.830508
50 MAG 0.452055 0.781818
51 2F8 0.452055 0.781818
52 MLD 0.444444 0.868852
53 NAG NM9 0.444444 0.875
54 FUC BGC GAL NAG 0.443299 0.851852
55 NOJ NAG NAG NAG 0.44086 0.816667
56 NOJ NAG NAG 0.44086 0.8
57 GYU 0.439024 0.770492
58 NAG MAN MMA 0.438202 0.836364
59 NAG MAN MAN MAN NAG 0.4375 0.888889
60 NGA GLA GAL BGC 0.43617 0.833333
61 DLD 0.430108 0.75
62 NG1 0.428571 0.698413
63 GN1 0.428571 0.698413
64 LEC NGA 0.427083 0.710145
65 6Y2 0.427083 0.710145
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 MAN NAG GAL 0.411111 0.833333
73 NAG GCU NAG GCU NAG GCU 5AX 0.41 0.890909
74 NAG BDP NAG BDP NAG BDP NAG 0.41 0.890909
75 3PV 0.41 0.857143
76 GAL NAG GAL 0.408602 0.803571
77 A2G GAL NAG FUC 0.405941 0.907407
78 A2G GAL BGC FUC 0.405941 0.851852
79 TNR 0.404762 0.789474
80 NAG NAG BMA 0.404255 0.827586
81 NAG NDG 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 0.764045 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 NAG AMU NAG AMV 0.55914 0.909091
8 MLD 0.532787 0.868852
9 MAN NAG 0.506173 0.833333
10 NAG NM9 0.5 0.875
11 NAG NAG 0.488372 0.810345
12 MAN MAN NAG 0.483516 0.803571
13 NGA GAL 0.481928 0.833333
14 NAG GAL 0.481928 0.833333
15 GAL NAG 0.481928 0.833333
16 NAG A2G 0.47619 0.888889
17 NAG NGA 0.47619 0.888889
18 MBG A2G 0.470588 0.836364
19 A2G MBG 0.470588 0.836364
20 NAG AMU ALA DGL 0.459459 0.862069
21 NAG NDG 0.458824 0.888889
22 CBS CBS 0.458824 0.888889
23 NAG GDL 0.458824 0.888889
24 CBS 0.458824 0.888889
25 NAG MBG 0.458824 0.836364
26 NDG NAG 0.448276 0.907407
27 NAG MAN MMA 0.445652 0.836364
28 NGA GAL BGC 0.43956 0.833333
29 NDG NAG NAG NAG 0.438202 0.907407
30 CTO 0.438202 0.907407
31 NDG NAG NAG 0.438202 0.907407
32 NDG NAG NAG NDG 0.438202 0.907407
33 NAG NAG NAG NDG 0.438202 0.907407
34 NAG NAG NAG NAG NAG 0.438202 0.907407
35 NAG NAG NAG NAG NDG 0.438202 0.907407
36 NAG NAG NAG NAG NAG NAG 0.438202 0.907407
37 NAG NAG NAG NAG NDG NAG 0.438202 0.907407
38 NAG NAG NAG 0.438202 0.907407
39 NAG NAG NDG 0.438202 0.907407
40 NDG NAG NAG NDG NAG 0.438202 0.907407
41 NAG NAG NAG NAG 0.438202 0.907407
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.438202 0.907407
43 NAG AH0 ALA DGL API DAL DAL 0.437037 0.9
44 AH0 0.435294 0.833333
45 NAG NGO 0.434783 0.927273
46 NAG MAN MAN 0.431579 0.833333
47 NAG MAN BMA 0.431579 0.833333
48 NAG MU2 0.428571 0.847458
49 FUC GL0 A2G 0.425532 0.851852
50 A2G GLA FUC 0.425532 0.851852
51 NGA GAL FUC 0.425532 0.851852
52 FUC GAL A2G 0.425532 0.851852
53 FUC GLA A2G 0.425532 0.851852
54 A2G GAL FUC 0.425532 0.851852
55 2F8 0.423077 0.781818
56 MAG 0.423077 0.781818
57 NAG GAL BGC 0.421053 0.833333
58 LEC NGA 0.42 0.735294
59 6Y2 0.42 0.735294
60 89A 0.419355 0.875
61 NOJ NAG NAG NAG 0.418367 0.847458
62 NOJ NAG NAG 0.418367 0.830508
63 NAG GCU NAG GCU NAG GCU 5AX 0.417476 0.925926
64 NAG BDP NAG BDP NAG BDP NAG 0.417476 0.925926
65 NAG MAN MAN MAN NAG 0.415842 0.888889
66 NAG NAG NAG NAG NAG NAG NAG 0.415842 0.830508
67 MA8 0.41573 0.745763
68 DLD 0.408163 0.777778
69 NAG GAL NAG 0.40625 0.888889
70 BGC FUC GAL FUC A2G 0.403846 0.87037
71 GLC FUC GAL FUC A2G 0.403846 0.87037
72 NG1 0.402439 0.698413
73 GN1 0.402439 0.698413
74 NGT NAG 0.402062 0.836066
75 NGA GLA GAL BGC 0.4 0.833333
76 A2G GAL BGC FUC 0.4 0.851852
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GVF; Ligand: NDG; Similar sites found: 17
This union binding pocket(no: 1) in the query (biounit: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A7V MAN 0.01308 0.40784 2.5788
2 3ZIU LSS 0.00907 0.4208 3.4384
3 3IGZ 3PG 0.003236 0.40468 4.45633
4 3IGZ 2PG 0.003236 0.40468 4.45633
5 4CU7 GIF 0.009482 0.40229 4.58453
6 5MW4 5JU 0.04336 0.40456 5.68862
7 4O08 PO6 0.01239 0.40763 5.919
8 3RF4 FUN 0.01319 0.4043 6.03448
9 3PE2 E1B 0.03972 0.40911 7.44986
10 1X38 IDD 0.00001969 0.53965 8.88252
11 5JU6 BGC 0.0004037 0.47239 15.4728
12 5K6N XYP 0.001294 0.43642 16.6189
13 4IID NOJ 0.001126 0.41425 17.192
14 4I3G BGC 0.0003484 0.47544 20.0573
15 4ZOA IFM 0.00001139 0.45856 22.3496
16 2X41 BGC 0.0009272 0.46115 23.4957
17 5JP0 BGC 0.000002285 0.58946 28.9398
Pocket No.: 2; Query (leader) PDB : 4GVF; Ligand: NAG; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A7V MAN 0.01308 0.40784 2.5788
2 3ZIU LSS 0.00907 0.4208 3.4384
3 3IGZ 3PG 0.003236 0.40468 4.45633
4 3IGZ 2PG 0.003236 0.40468 4.45633
5 4CU7 GIF 0.009482 0.40229 4.58453
6 5MW4 5JU 0.04336 0.40456 5.68862
7 4O08 PO6 0.01239 0.40763 5.919
8 3RF4 FUN 0.01319 0.4043 6.03448
9 3PE2 E1B 0.03972 0.40911 7.44986
10 1X38 IDD 0.00001969 0.53965 8.88252
11 5JU6 BGC 0.0004037 0.47239 15.4728
12 5K6N XYP 0.001294 0.43642 16.6189
13 4IID NOJ 0.001126 0.41425 17.192
14 4I3G BGC 0.0003484 0.47544 20.0573
15 4ZOA IFM 0.00001139 0.45856 22.3496
16 2X41 BGC 0.0009272 0.46115 23.4957
17 5JP0 BGC 0.000002285 0.58946 28.9398
Pocket No.: 3; Query (leader) PDB : 4GVF; Ligand: NAG; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L7G 6QE 0.01145 0.41018 2.29508
2 5JCA NDP 0.04494 0.41389 2.86533
3 1YRE COA 0.01246 0.40138 4.06091
Pocket No.: 4; Query (leader) PDB : 4GVF; Ligand: NDG; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L7G 6QE 0.01145 0.41018 2.29508
2 5JCA NDP 0.04494 0.41389 2.86533
3 1YRE COA 0.01246 0.40138 4.06091
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