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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MES B:403;
Invalid;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
NAG A:402;
B:402;
Valid;
Valid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NDG A:401;
B:401;
Valid;
Valid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
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: NAG; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA 1 1
2 NAG 1 1
3 A2G 1 1
4 BM3 1 1
5 HSQ 1 1
6 NDG 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 STZ 0.612245 0.65
11 4QY 0.591837 0.735849
12 BMX 0.591837 0.735849
13 16G 0.591837 0.735849
14 9C1 0.58 0.886364
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NDG NAG 0.54386 0.833333
18 CBS 0.54386 0.833333
19 NAG GDL 0.54386 0.833333
20 CBS CBS 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 MAG 0.530612 0.909091
24 2F8 0.530612 0.909091
25 NDG GAL 0.517857 0.888889
26 NLC 0.517857 0.888889
27 GAL NDG 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 4UZ 0.508475 0.808511
32 NAG NAG NAG NAG NDG 0.508197 0.816327
33 NDG NAG NAG NAG 0.508197 0.816327
34 NAG NAG NDG 0.508197 0.816327
35 NAG NAG NDG NAG 0.508197 0.816327
36 CTO 0.508197 0.816327
37 NDG NAG NAG NDG 0.508197 0.816327
38 NAG NAG NAG NDG 0.508197 0.816327
39 NDG NAG NAG 0.508197 0.816327
40 NAG NAG NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 MQG 0.5 0.698113
44 NBG 0.5 0.951219
45 GAL NGA 0.491228 0.888889
46 A2G GAL 0.491228 0.888889
47 GAL A2G 0.491228 0.888889
48 AMU 0.490909 0.930233
49 NG1 0.490566 0.754717
50 GN1 0.490566 0.754717
51 NAG GAL 0.474576 0.888889
52 GAL NAG 0.474576 0.888889
53 NAG FUC 0.474576 0.866667
54 NAG GAL NAG 0.455882 0.833333
55 3YW 0.448276 0.930233
56 GLA GAL NAG 0.446154 0.888889
57 MAN BMA NAG 0.446154 0.888889
58 NGA GAL 0.428571 0.869565
59 FUC GAL NAG 0.426471 0.869565
60 GAL NAG FUC 0.426471 0.869565
61 DR2 0.426471 0.869565
62 NAG GAL FUC 0.426471 0.869565
63 NDG GAL FUC 0.426471 0.869565
64 FUC GAL NDG 0.426471 0.869565
65 FUL GAL NAG 0.426471 0.869565
66 G6S NAG 0.426471 0.645161
67 TNR 0.42623 0.833333
68 GYU 0.42623 0.740741
69 GAL NGA A2G 0.424242 0.833333
70 NAG BDP 0.421875 0.851064
71 NAG MBG 0.419355 0.851064
72 NGA GAL BGC 0.41791 0.888889
73 NAG NDG 0.415385 0.784314
74 NAG NAG 0.415385 0.784314
75 AZC 0.415094 0.795918
76 SN5 SN5 0.412698 0.705882
77 A2G MBG 0.412698 0.851064
78 MBG A2G 0.412698 0.851064
79 HS2 0.411765 0.8125
80 5AX 0.411765 0.866667
81 NAG MAN BMA 0.411765 0.888889
82 6ZC 0.409091 0.655738
83 LEC 0.409091 0.655738
84 TCG 0.408451 0.689655
85 GAL BGC NAG GAL 0.408451 0.888889
86 NAG MAN 0.40625 0.851064
87 WOO 0.404762 0.7
88 MAN 0.404762 0.7
89 GAL 0.404762 0.7
90 BGC 0.404762 0.7
91 BMA 0.404762 0.7
92 GLA 0.404762 0.7
93 ALL 0.404762 0.7
94 GLC 0.404762 0.7
95 GXL 0.404762 0.7
96 GIV 0.404762 0.7
97 NAG AMU 0.402778 0.8
98 NAG MUB 0.402778 0.8
99 NAG A2G GAL 0.402778 0.833333
100 A2G GAL FUC 0.4 0.869565
101 FUC GLA A2G 0.4 0.869565
102 DR3 0.4 0.869565
103 A2G GLA FUC 0.4 0.869565
104 NGA GAL FUC 0.4 0.869565
105 FUC GAL A2G 0.4 0.869565
Ligand no: 2; Ligand: NDG; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA 1 1
2 NAG 1 1
3 A2G 1 1
4 BM3 1 1
5 HSQ 1 1
6 NDG 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 STZ 0.612245 0.65
11 4QY 0.591837 0.735849
12 BMX 0.591837 0.735849
13 16G 0.591837 0.735849
14 9C1 0.58 0.886364
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NDG NAG 0.54386 0.833333
18 CBS 0.54386 0.833333
19 NAG GDL 0.54386 0.833333
20 CBS CBS 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 MAG 0.530612 0.909091
24 2F8 0.530612 0.909091
25 NDG GAL 0.517857 0.888889
26 NLC 0.517857 0.888889
27 GAL NDG 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 4UZ 0.508475 0.808511
32 NAG NAG NAG NAG NDG 0.508197 0.816327
33 NDG NAG NAG NAG 0.508197 0.816327
34 NAG NAG NDG 0.508197 0.816327
35 NAG NAG NDG NAG 0.508197 0.816327
36 CTO 0.508197 0.816327
37 NDG NAG NAG NDG 0.508197 0.816327
38 NAG NAG NAG NDG 0.508197 0.816327
39 NDG NAG NAG 0.508197 0.816327
40 NAG NAG NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 MQG 0.5 0.698113
44 NBG 0.5 0.951219
45 GAL NGA 0.491228 0.888889
46 A2G GAL 0.491228 0.888889
47 GAL A2G 0.491228 0.888889
48 AMU 0.490909 0.930233
49 NG1 0.490566 0.754717
50 GN1 0.490566 0.754717
51 NAG GAL 0.474576 0.888889
52 GAL NAG 0.474576 0.888889
53 NAG FUC 0.474576 0.866667
54 NAG GAL NAG 0.455882 0.833333
55 3YW 0.448276 0.930233
56 GLA GAL NAG 0.446154 0.888889
57 MAN BMA NAG 0.446154 0.888889
58 NGA GAL 0.428571 0.869565
59 FUC GAL NAG 0.426471 0.869565
60 GAL NAG FUC 0.426471 0.869565
61 DR2 0.426471 0.869565
62 NAG GAL FUC 0.426471 0.869565
63 NDG GAL FUC 0.426471 0.869565
64 FUC GAL NDG 0.426471 0.869565
65 FUL GAL NAG 0.426471 0.869565
66 G6S NAG 0.426471 0.645161
67 TNR 0.42623 0.833333
68 GYU 0.42623 0.740741
69 GAL NGA A2G 0.424242 0.833333
70 NAG BDP 0.421875 0.851064
71 NAG MBG 0.419355 0.851064
72 NGA GAL BGC 0.41791 0.888889
73 NAG NDG 0.415385 0.784314
74 NAG NAG 0.415385 0.784314
75 AZC 0.415094 0.795918
76 SN5 SN5 0.412698 0.705882
77 A2G MBG 0.412698 0.851064
78 MBG A2G 0.412698 0.851064
79 HS2 0.411765 0.8125
80 5AX 0.411765 0.866667
81 NAG MAN BMA 0.411765 0.888889
82 6ZC 0.409091 0.655738
83 LEC 0.409091 0.655738
84 TCG 0.408451 0.689655
85 GAL BGC NAG GAL 0.408451 0.888889
86 NAG MAN 0.40625 0.851064
87 WOO 0.404762 0.7
88 MAN 0.404762 0.7
89 GAL 0.404762 0.7
90 BGC 0.404762 0.7
91 BMA 0.404762 0.7
92 GLA 0.404762 0.7
93 ALL 0.404762 0.7
94 GLC 0.404762 0.7
95 GXL 0.404762 0.7
96 GIV 0.404762 0.7
97 NAG AMU 0.402778 0.8
98 NAG MUB 0.402778 0.8
99 NAG A2G GAL 0.402778 0.833333
100 A2G GAL FUC 0.4 0.869565
101 FUC GLA A2G 0.4 0.869565
102 DR3 0.4 0.869565
103 A2G GLA FUC 0.4 0.869565
104 NGA GAL FUC 0.4 0.869565
105 FUC GAL A2G 0.4 0.869565
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: 27
This union binding pocket(no: 1) in the query (biounit: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3L02 CP 1.7192
2 3L02 SN0 1.7192
3 5MWY YNU 2.29508
4 5A7V MAN 2.5788
5 5HCV 60R 2.72374
6 5E58 CPZ 2.86533
7 3ZIU LSS 3.4384
8 3IGZ 3PG 4.45633
9 3IGZ 2PG 4.45633
10 1OX5 1PR 4.58453
11 4CU7 GIF 4.58453
12 5MW4 5JU 5.68862
13 4O08 PO6 5.919
14 3RF4 FUN 6.03448
15 1SR7 MOF 6.56371
16 1O5Q PYR 6.88525
17 1X39 IDE 8.88252
18 1O98 2PG 11.4613
19 5Z9S BGC 12.1859
20 5JU6 BGC 15.4728
21 5K6N XYP 16.6189
22 4IID NOJ 17.192
23 4I3G BGC 20.0573
24 4ZOA IFM 22.3496
25 2X41 BGC 23.4957
26 5JP0 BGC 28.9398
27 5XXM LGC 33.2378
Pocket No.: 2; Query (leader) PDB : 4GVF; Ligand: NAG; Similar sites found with APoc: 27
This union binding pocket(no: 2) in the query (biounit: 4gvf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3L02 CP 1.7192
2 3L02 SN0 1.7192
3 5MWY YNU 2.29508
4 5A7V MAN 2.5788
5 5HCV 60R 2.72374
6 5E58 CPZ 2.86533
7 3ZIU LSS 3.4384
8 3IGZ 2PG 4.45633
9 3IGZ 3PG 4.45633
10 1OX5 1PR 4.58453
11 4CU7 GIF 4.58453
12 5MW4 5JU 5.68862
13 4O08 PO6 5.919
14 3RF4 FUN 6.03448
15 1SR7 MOF 6.56371
16 1O5Q PYR 6.88525
17 1X39 IDE 8.88252
18 1O98 2PG 11.4613
19 5Z9S BGC 12.1859
20 5JU6 BGC 15.4728
21 5K6N XYP 16.6189
22 4IID NOJ 17.192
23 4I3G BGC 20.0573
24 4ZOA IFM 22.3496
25 2X41 BGC 23.4957
26 5JP0 BGC 28.9398
27 5XXM LGC 33.2378
Pocket No.: 3; Query (leader) PDB : 4GVF; Ligand: NAG; Similar sites found with APoc: 13
This union binding pocket(no: 3) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4D1J DGJ 1.7192
2 4RP9 ASC 2.00573
3 5L7G 6QE 2.29508
4 1HG4 LPP 2.50896
5 5JCA NDP 2.86533
6 3ZOK NAD 3.4384
7 1YRE COA 4.06091
8 1WUB OTP 5.05618
9 2O4J VD4 5.13699
10 1DB1 VDX 7.33591
11 2E2R 2OH 7.37705
12 3MWS 017 9.09091
13 2FTB OLA 11.2
Pocket No.: 4; Query (leader) PDB : 4GVF; Ligand: NDG; Similar sites found with APoc: 13
This union binding pocket(no: 4) in the query (biounit: 4gvf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4D1J DGJ 1.7192
2 4RP9 ASC 2.00573
3 5L7G 6QE 2.29508
4 1HG4 LPP 2.50896
5 5JCA NDP 2.86533
6 3ZOK NAD 3.4384
7 1YRE COA 4.06091
8 1WUB OTP 5.05618
9 2O4J VD4 5.13699
10 1DB1 VDX 7.33591
11 2E2R 2OH 7.37705
12 3MWS 017 9.09091
13 2FTB OLA 11.2
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