Receptor
PDB id Resolution Class Description Source Keywords
5YMS 2.1 Å NON-ENZYME: OTHER STRUCTURAL BASIS OF GLYCAN SPECIFICITY AND IDENTIFICATION OF GLYCAN BINDING CAVITY IN HUMAN P[19] ROTAVIRUS HUMAN ROTAVIRUS A P[19] ROTAVIRUS P[6] ROTAVIRUS VP8* MUCIN CORE2CORE 2 LATETRAROSETETRAOSE (LNT) VIRAL PROTEIN
Ref.: GLYCAN BINDING SPECIFICITY AND MECHANISM OF HUMAN A PORCINE P[6]/P[19] ROTAVIRUS VP8*S. J. VIROL. V. 92 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A2G GAL H:601;
F:601;
Valid;
Valid;
none;
none;
submit data
586.544 n/a O=C(N...
NAG B:601;
D:601;
A:601;
C:601;
G:601;
E:601;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.067;
Atoms found LESS than expected: % Diff = 0.067;
Atoms found LESS than expected: % Diff = 0.067;
Atoms found LESS than expected: % Diff = 0.067;
Atoms found LESS than expected: % Diff = 0.067;
Atoms found LESS than expected: % Diff = 0.067;
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
5VKI 1.9 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF P[19] ROTAVIRUS VP8* COMPLEXED WITH MUC HUMAN ROTAVIRUS A COMPLEX P[19]VP8* MUCIN CORE 2 VIRAL PROTEIN
Ref.: STRUCTURAL BASIS OF GLYCAN SPECIFICITY OF P[19] VP8 IMPLICATIONS FOR ROTAVIRUS ZOONOSIS AND EVOLUTION. PLOS PATHOG. V. 13 06707 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5YMS - NAG C8 H15 N O6 CC(=O)N[C@....
2 5YMT - GAL NAG GAL GLC n/a n/a
3 5VKS - GLC NAG GAL GAL FUC n/a n/a
4 5VKI - THR NGA GAL NAG n/a n/a
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3TB0 - MN0 C12 H21 N O10 CO[C@@]1(C....
2 2P3I Kd = 0.33 mM MNA C12 H21 N O9 CC(=O)N[C@....
3 2P3J - MNA C12 H21 N O9 CC(=O)N[C@....
4 2P3K - MNA C12 H21 N O9 CC(=O)N[C@....
5 5YMS - NAG C8 H15 N O6 CC(=O)N[C@....
6 5YMT - GAL NAG GAL GLC n/a n/a
7 5VKS - GLC NAG GAL GAL FUC n/a n/a
8 5VKI - THR NGA GAL NAG n/a n/a
9 3TAY Kd = 0.42 mM MN0 C12 H21 N O10 CO[C@@]1(C....
10 3SIT - SIA GAL GLC n/a n/a
11 5CA6 - PLM C16 H32 O2 CCCCCCCCCC....
12 2I2S - MNA C12 H21 N O9 CC(=O)N[C@....
13 3SIS - MN0 GAL GLC n/a n/a
14 5VX9 - FUC GAL NAG GAL BGC n/a n/a
15 5VX5 - FUC GAL NAG GAL BGC n/a n/a
16 1KQR - MNA C12 H21 N O9 CC(=O)N[C@....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3TB0 - MN0 C12 H21 N O10 CO[C@@]1(C....
2 2P3I Kd = 0.33 mM MNA C12 H21 N O9 CC(=O)N[C@....
3 2P3J - MNA C12 H21 N O9 CC(=O)N[C@....
4 2P3K - MNA C12 H21 N O9 CC(=O)N[C@....
5 4DS0 - A2G GAL NAG FUC n/a n/a
6 4DRV - A2G GLA FUC n/a n/a
7 4YG0 - GAL NAG GAL BGC n/a n/a
8 4YFZ - GAL NAG GAL BGC n/a n/a
9 5YMS - NAG C8 H15 N O6 CC(=O)N[C@....
10 5YMT - GAL NAG GAL GLC n/a n/a
11 5VKS - GLC NAG GAL GAL FUC n/a n/a
12 5VKI - THR NGA GAL NAG n/a n/a
13 3TAY Kd = 0.42 mM MN0 C12 H21 N O10 CO[C@@]1(C....
14 3SIT - SIA GAL GLC n/a n/a
15 5CA6 - PLM C16 H32 O2 CCCCCCCCCC....
16 2I2S - MNA C12 H21 N O9 CC(=O)N[C@....
17 3SIS - MN0 GAL GLC n/a n/a
18 4YG6 - GAL NAG GAL BGC n/a n/a
19 5CB7 - A2G GLA FUC n/a n/a
20 5VX9 - FUC GAL NAG GAL BGC n/a n/a
21 5VX5 - FUC GAL NAG GAL BGC n/a n/a
22 1KQR - MNA C12 H21 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG A2G GAL; Similar ligands found: 151
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG A2G GAL 1 1
2 A2G GAL 0.681159 0.9375
3 GAL NGA 0.681159 0.9375
4 GAL A2G 0.681159 0.9375
5 THR NGA GAL NAG 0.629214 0.941176
6 NAG A2G 0.608108 1
7 NAG NGA 0.608108 1
8 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.571429 1
9 1GN ACY GAL ACY 1GN BGC GAL BGC 0.571429 1
10 GAL A2G MBN 0.523256 0.9
11 NAG BDP NAG BDP NAG BDP NAG 0.516129 0.96
12 NAG MAN BMA MAN NAG GAL 0.51 1
13 NLC 0.506494 0.9375
14 GAL NDG 0.506494 0.9375
15 NDG GAL 0.506494 0.9375
16 GAL MGC 0.506494 0.938776
17 NAG MAN MAN 0.505747 0.9375
18 GAL NDG FUC 0.494118 0.958333
19 FUC NDG GAL 0.494118 0.958333
20 NAG NAG BMA MAN MAN 0.489796 1
21 GAL BGC NAG GAL 0.488636 0.9375
22 NGA SER GAL 0.488372 0.903846
23 GAL SER A2G 0.488372 0.903846
24 A2G SER GAL 0.488372 0.903846
25 GAL TNR 0.488372 0.903846
26 NAG BDP 0.487805 0.9
27 NAG MAN MAN MAN NAG 0.483871 1
28 DR3 0.482759 0.958333
29 NAG MAN BMA NDG MAN NAG GAL 0.481132 0.979592
30 NAG NAG BMA MAN MAN NAG GAL NAG 0.476636 0.979592
31 M5G 0.476636 1
32 NAG GAL 0.475 0.9375
33 GAL NAG 0.475 0.9375
34 TNR 0.475 0.882353
35 3YW 0.474359 0.857143
36 NAG BMA MAN MAN MAN MAN 0.474227 0.9375
37 BMA Z4Y NAG 0.473118 0.918367
38 MAN BMA NAG 0.470588 0.9375
39 GLA GAL NAG 0.470588 0.9375
40 NAG GDL 0.469136 1
41 CBS CBS 0.469136 1
42 NDG NAG 0.469136 1
43 CBS 0.469136 1
44 A2G GAL FUC 0.465909 0.958333
45 FUC GAL A2G 0.465909 0.958333
46 FUC GLA A2G 0.465909 0.958333
47 A2G GLA FUC 0.465909 0.958333
48 NGA GAL FUC 0.465909 0.958333
49 NGA GAL BGC 0.465116 0.9375
50 MAN BMA MAN 0.4625 0.6875
51 GAL NAG GAL NAG GAL NAG 0.461538 0.979592
52 NAG MAN MAN MAN NAG GAL NAG GAL 0.461538 0.979592
53 MAN BMA NAG NAG MAN NAG GAL GAL 0.461538 0.979592
54 NAG GAL GAL NAG 0.461538 1
55 NAG GAL NAG 0.460674 1
56 NAG GAL BGC 0.460674 0.9375
57 GAL NAG MAN 0.45977 0.9375
58 3PV 0.453608 0.884615
59 GAL NGA A2G 0.453488 1
60 2F8 0.452055 0.877551
61 MAG 0.452055 0.877551
62 NGA GLA GAL BGC 0.451613 0.9375
63 BGC GAL NAG GAL 0.450549 0.9375
64 GAL NAG GAL GLC 0.450549 0.9375
65 NAG MUB 0.450549 0.96
66 NAG AMU 0.450549 0.96
67 8VZ 0.45 0.979592
68 WZ5 0.45 0.938776
69 GC4 NAG 0.448276 0.9
70 GN1 0.447368 0.741379
71 NG1 0.447368 0.741379
72 NAG NAG NAG NAG NAG NAG 0.447059 0.979592
73 NDG NAG NAG NAG 0.447059 0.979592
74 NAG NAG NDG NAG 0.447059 0.979592
75 NAG NAG NAG NDG 0.447059 0.979592
76 NAG NAG NDG 0.447059 0.979592
77 CTO 0.447059 0.979592
78 NAG NAG NAG NAG NAG NAG NAG NAG 0.447059 0.979592
79 NAG NAG NAG NAG NAG 0.447059 0.979592
80 NDG NAG NAG 0.447059 0.979592
81 NDG NAG NAG NDG 0.447059 0.979592
82 NAG NAG NAG NAG NDG 0.447059 0.979592
83 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.446602 0.9375
84 A2G MBG 0.445783 0.938776
85 MBG A2G 0.445783 0.938776
86 NAG GAL GAL NAG GAL 0.445652 1
87 GAL A2G THR 0.444444 0.941176
88 UCD 0.443182 0.882353
89 GLC GAL NAG GAL 0.44086 0.9375
90 LAT NAG GAL 0.44086 0.9375
91 NGA GAL 0.440476 0.88
92 NAG GAL FUC FUC A2G 0.44 0.979592
93 FUC GAL NAG A2G FUC 0.44 0.979592
94 GAL NAG GAL 0.43956 0.9
95 NGA GCD 0.438202 0.865385
96 GAD NDG 0.438202 0.865385
97 GCD NGA 0.438202 0.865385
98 NAG GAD 0.438202 0.865385
99 NAG MBG 0.433735 0.938776
100 NAG BMA 0.433735 0.846154
101 GAL NGA GLA BGC GAL 0.431579 0.9375
102 MAN BMA MAN MAN MAN 0.430233 0.6875
103 M5S 0.430233 0.6875
104 NAG NAG BMA MAN NAG 0.429907 0.90566
105 NAG BMA NAG MAN MAN NAG NAG 0.429907 0.979592
106 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.428571 1
107 NAG MAN BMA 0.426966 0.9375
108 G6S NAG 0.422222 0.71875
109 GCD NG6 0.421053 0.656716
110 NG6 GCD 0.421053 0.656716
111 NAG NAG BMA 0.419355 0.923077
112 NAG NDG BMA 0.419355 0.923077
113 MAN MAN MAN MAN 0.418605 0.6875
114 GAL LOG 0.418605 0.793103
115 MAN MAN BMA MAN 0.418605 0.6875
116 MAN MMA MAN 0.416667 0.693878
117 BMA MAN MAN MAN MAN 0.41573 0.6875
118 FUC BGC GAL NAG 0.414141 0.958333
119 NAG NDG 0.413793 0.903846
120 NAG NAG 0.413793 0.903846
121 GAL NAG GAL BGC 0.412371 0.9
122 MAG FUC GAL 0.411111 0.92
123 GAL A2G NPO 0.410526 0.734375
124 NPO A2G GAL 0.410526 0.734375
125 FUC GAL NAG FUC 0.408602 0.938776
126 GAL NAG FUC FUC 0.408602 0.938776
127 FUC GAL NDG FUC 0.408602 0.938776
128 BDZ 0.408602 0.938776
129 BCW 0.408602 0.938776
130 GAL NDG FUC FUC 0.408602 0.938776
131 FUC NAG GAL FUC 0.408602 0.938776
132 FUC NDG GAL FUC 0.408602 0.938776
133 NAG MAN 0.406977 0.938776
134 A2G GAL NAG FUC 0.405941 0.979592
135 A2G GAL BGC FUC 0.405941 0.958333
136 FUC GAL NAG A2G 0.405941 0.979592
137 FUC GAL GLA 0.404762 0.708333
138 GLA GLA FUC 0.404762 0.708333
139 FUC GLA GLA 0.404762 0.708333
140 GLA GAL FUC 0.404762 0.708333
141 GAL GAL FUC 0.404762 0.708333
142 AH0 NAG 0.404255 0.888889
143 FUC C4W NAG BMA 0.403846 0.923077
144 A2G 0.402778 0.833333
145 HSQ 0.402778 0.833333
146 NDG 0.402778 0.833333
147 NAG 0.402778 0.833333
148 BM3 0.402778 0.833333
149 NGA 0.402778 0.833333
150 GAL NAG GAL FUC 0.402062 0.958333
151 GLA NAG GAL FUC 0.402062 0.958333
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VKI; Ligand: THR NGA GAL NAG; 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: 5vki.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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