Receptor
PDB id Resolution Class Description Source Keywords
5VX9 1.82 Å NON-ENZYME: OTHER VP8* OF P[6] HUMAN ROTAVIRUS RV3 IN COMPLEX WITH LNFP1 HUMAN ROTAVIRUS A GLYCAN HBGA ROTAVIRUS VIRAL PROTEIN
Ref.: GLYCAN RECOGNITION IN GLOBALLY DOMINANT HUMAN ROTAV NAT COMMUN V. 9 2631 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:306;
A:307;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
BGC GAL NAG GAL FUC B:1;
 Valid;
 none;
 submit data
853.774 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VX9 1.82 Å NON-ENZYME: OTHER VP8* OF P[6] HUMAN ROTAVIRUS RV3 IN COMPLEX WITH LNFP1 HUMAN ROTAVIRUS A GLYCAN HBGA ROTAVIRUS VIRAL PROTEIN
Ref.: GLYCAN RECOGNITION IN GLOBALLY DOMINANT HUMAN ROTAV NAT COMMUN V. 9 2631 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5VX9 - BGC GAL NAG GAL FUC n/a n/a
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 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 - A2G GAL NAG n/a n/a
6 5YMT - GLC GAL NAG GAL n/a n/a
7 5VKS - GLC GAL NAG GAL FUC n/a n/a
8 5VKI - NGA THR GAL NAG n/a n/a
9 3TAY Kd = 0.42 mM MN0 C12 H21 N O10 CO[C@@]1(C....
10 3SIT - GLC GAL SIA n/a n/a
11 5CA6 - PLM C16 H32 O2 CCCCCCCCCC....
12 2I2S - MNA C12 H21 N O9 CC(=O)N[C@....
13 3SIS - GLC GAL NGC n/a n/a
14 5VX9 - BGC GAL NAG GAL FUC n/a n/a
15 5VX5 - BGC GAL NAG GAL FUC n/a n/a
16 1KQR - MNA C12 H21 N O9 CC(=O)N[C@....
17 6H9Y - NAG GAL n/a n/a
18 6K2O - GAL NAG GAL FUC n/a n/a
19 6H9W - CIT C6 H8 O7 C(C(=O)O)C....
20 6K2N - A2G GAL NAG n/a n/a
21 6HA0 - NAG GAL FUC n/a n/a
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 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 - NAG GAL FUC A2G n/a n/a
6 4DRV - GLA FUC A2G n/a n/a
7 4YG0 - BGC GAL NAG GAL n/a n/a
8 4YFZ - BGC GAL NAG GAL n/a n/a
9 5YMS - A2G GAL NAG n/a n/a
10 5YMT - GLC GAL NAG GAL n/a n/a
11 5VKS - GLC GAL NAG GAL FUC n/a n/a
12 5VKI - NGA THR GAL NAG n/a n/a
13 3TAY Kd = 0.42 mM MN0 C12 H21 N O10 CO[C@@]1(C....
14 3SIT - GLC GAL SIA n/a n/a
15 5CA6 - PLM C16 H32 O2 CCCCCCCCCC....
16 2I2S - MNA C12 H21 N O9 CC(=O)N[C@....
17 3SIS - GLC GAL NGC n/a n/a
18 4YG6 - BGC GAL NAG GAL n/a n/a
19 5CB7 - A2G GAL FUC n/a n/a
20 5VX9 - BGC GAL NAG GAL FUC n/a n/a
21 5VX5 - BGC GAL NAG GAL FUC n/a n/a
22 1KQR - MNA C12 H21 N O9 CC(=O)N[C@....
23 6H9Y - NAG GAL n/a n/a
24 6K2O - GAL NAG GAL FUC n/a n/a
25 6H9W - CIT C6 H8 O7 C(C(=O)O)C....
26 6K2N - A2G GAL NAG n/a n/a
27 6HA0 - NAG GAL FUC n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC GAL NAG GAL FUC; Similar ligands found: 124
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL NAG GAL FUC 1 1
2 BGC GAL NAG GAL FUC FUC 0.840909 0.978723
3 GLC GAL NAG GAL FUC GLA 0.831461 1
4 GLC GAL NAG GAL FUC A2G 0.787234 0.938776
5 BGC GAL NAG GAL 0.768293 0.978261
6 GLA NAG GAL FUC 0.752941 1
7 BGC GAL GLA NGA GAL 0.732558 0.978261
8 BGC GAL FUC 0.675 0.73913
9 GLC GAL BGC FUC 0.675 0.73913
10 BGC GAL NAG 0.662791 0.978261
11 BGC GAL GLA NGA 0.644444 0.978261
12 BGC GAL NGA GAL 0.643678 0.978261
13 GAL NAG GAL FUC 0.634409 0.958333
14 NAG GAL FUC 0.632184 1
15 BGC GAL FUC A2G 0.631579 1
16 GAL NAG GAL FUC FUC 0.62766 0.978723
17 BGC FUC GAL NAG GAL 0.622449 1
18 NAG GAL FUC A2G 0.62069 1
19 BGC FUC GAL NAG 0.610526 1
20 BGC GAL SIA NGA GAL FUC 0.598361 0.884615
21 BGC GAL FUC GLA 0.577778 0.73913
22 NAG GAL FUC FUC 0.565217 0.978723
23 NDG FUC GAL FUC 0.565217 0.978723
24 BGC GAL GLA 0.560976 0.717391
25 NAG NAG BMA MAN NAG 0.56 0.938776
26 GAL NAG FUC GAL 0.552083 1
27 NAG GAL GAL 0.550562 0.978261
28 MAG FUC GAL FUC 0.548387 0.958333
29 MAG GAL FUC FUC 0.548387 0.958333
30 NAG GAL FUC GLA 0.546392 1
31 BGC GAL NAG NAG GAL GAL 0.543689 0.958333
32 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.538462 0.92
33 NAG GAL NAG 0.537634 0.958333
34 NAG GAL NAG GAL NAG GAL 0.536842 0.938776
35 NAG GAL NAG GAL 0.536842 0.958333
36 GAL NAG GAL NAG GAL 0.536842 0.958333
37 BGC BGC BGC BGC BGC BGC BGC BGC 0.534884 0.717391
38 BGC GAL NGA 0.527473 0.978261
39 NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.514019 0.978261
40 BGC FUC GAL FUC A2G 0.509804 0.978723
41 NAG BMA MAN MAN MAN MAN MAN MAN MAN MAN 0.509259 0.978261
42 NAG BMA MAN MAN NAG GAL NAG GAL 0.5 0.938776
43 BGC GAL GLA NGA GAL SIA 0.495935 0.884615
44 MAN MAN MAN GLC 0.494382 0.717391
45 NDG BMA MAN MAN NAG GAL NAG 0.491228 0.938776
46 NAG FUC GAL 0.489362 1
47 NAG FUC 0.488636 0.978261
48 NDG BMA MAN MAN NAG MAN MAN 0.486957 0.958333
49 NAG NAG BMA MAN MAN NAG GAL NAG 0.486957 0.938776
50 GAL NAG GAL 0.484211 0.978261
51 MMA MAN NAG 0.484211 0.978723
52 GAL NGA A2G 0.483871 0.958333
53 GAL FUC A2G 0.479167 1
54 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.478632 0.958333
55 C4W NAG FUC BMA MAN 0.473684 0.884615
56 BGC GAL SIA NGA GAL 0.472 0.884615
57 1GN ACY GAL 1GN BGC ACY GAL BGC 0.471698 0.958333
58 NAG GAL FUC FUC A2G 0.46729 0.938776
59 NAG FUC GAL FUC A2G 0.46729 0.938776
60 BGC FUC GAL 0.466667 0.73913
61 GLC BGC FUC GAL 0.466667 0.73913
62 NAG GAL 0.465909 0.978261
63 BMA MAN MAN NAG GAL NAG 0.464286 0.958333
64 BMA MAN NAG 0.463918 0.978261
65 NAG NON FUC GAL FUC 0.463636 0.836364
66 NAG NAG FUL BMA MAN MAN NAG GAL 0.459677 0.867925
67 MAN NAG GAL 0.458333 0.978261
68 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.457364 0.793103
69 BGC GAL NAG GAL SIA 0.453125 0.867925
70 NAG NAG BMA MAN 0.45283 0.884615
71 XYS GAL FUC 0.452632 0.723404
72 C4W NAG FUC BMA MAN MAN NAG NAG 0.452381 0.884615
73 MAN NAG PO4 NGA PO4 0.45098 0.807018
74 GAL NGA GAL SIA 0.45 0.884615
75 MGC GAL 0.449438 0.978723
76 RAM MAN GLA ABE RAM MAN GLA 0.448276 0.714286
77 MAG SGA FUC 0.447619 0.730159
78 GLC GLC GLC GLC BGC GLC GLC 0.447059 0.717391
79 MAN BMA BMA BMA BMA BMA BMA 0.447059 0.717391
80 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.447059 0.717391
81 NAG NAG BMA MAN MAN MAN MAN 0.446281 0.884615
82 NDG GAL FUC FUC 0.445545 0.9
83 C4W NAG FUC BMA MAN MAN NAG 0.445312 0.884615
84 GLA NAG FUC GAL 0.443396 0.978723
85 BGC GAL SIA NGA GAL SIA 0.440945 0.884615
86 MAG FUC SGA 0.433962 0.692308
87 A2G GAL 0.433333 0.978261
88 NAG NAG MAN MAN MAN 0.432432 0.958333
89 NAG BMA MAN MAN MAN MAN 0.431193 0.978261
90 A2G MBN GAL 0.425743 0.9375
91 NAG GAL BGC GAL 0.425743 0.978261
92 ACG 0.424779 0.82
93 MAN MAN MAN NAG NAG 0.424528 0.958333
94 GAL NGA GAL SIA SIA 0.424242 0.867925
95 GAL FUC GAL 0.423913 0.73913
96 NDG GLA NAG GLC RAM 0.420168 0.938776
97 NDG NAG GLA NAG GLC RAM 0.420168 0.938776
98 MBG NAG 0.419355 0.978723
99 NAG NAG BMA MAN MAN NAG NAG 0.418033 0.867925
100 TVD GAL 0.417582 0.938776
101 BGC GLC GLD GLC ACI GLD GLC ACI G6D 0.415929 0.773585
102 MAN MAN NAG 0.415842 0.9375
103 OPM MAN MAN 0.414141 0.641509
104 GLC GLC AC1 0.413043 0.833333
105 HSH A2G FUC 0.412844 0.836364
106 BGC BGC BGC BGC BGC BGC 0.409091 0.717391
107 BGC BGC BGC BGC BGC 0.409091 0.717391
108 BGC BGC BGC BGC BGC BGC BGC 0.409091 0.717391
109 BGC BGC BGC 0.409091 0.717391
110 GLC BGC BGC BGC 0.409091 0.717391
111 BHE 0.408163 0.648148
112 C4W NAG FUC BMA MAN NAG GAL 0.408 0.793103
113 GLC BGC G6D ACI 0.407407 0.82
114 C4W NAG FUC BMA 0.40708 0.884615
115 GLC GAL EMB GAL MEC 0.40708 0.736842
116 BGC GLC AGL GLC GLC GLC 0.40566 0.916667
117 GLC GLC G6D ACI 0.405405 0.788462
118 GAL NAG FUC GAL SIA 0.40458 0.884615
119 BMA BMA BMA BMA 0.404255 0.717391
120 GDL NAG 0.404255 0.958333
121 ARE 0.403509 0.82
122 AAO 0.403509 0.82
123 4YA 0.402062 0.648148
124 NAG BDP NAG BDP NAG BDP NAG 0.4 0.92
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL NAG GAL FUC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 GLC GAL NAG GAL FUC 0.9038
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VX9; Ligand: BGC GAL NAG GAL FUC; 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: 5vx9.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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