Receptor
PDB id Resolution Class Description Source Keywords
3NXD 2 Å NON-ENZYME: OTHER JC POLYOMAVIRUS VP1 IN COMPLEX WITH LSTC JC POLYOMAVIRUS BETA-SANDWICH WITH JELLY ROLL TOPOLOGY MAJOR CAPSID PROTEINPROTEIN
Ref.: STRUCTURE-FUNCTION ANALYSIS OF THE HUMAN JC POLYOMA ESTABLISHES THE LSTC PENTASACCHARIDE AS A FUNCTIONA RECEPTOR MOTIF. CELL HOST MICROBE V. 8 309 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BGC GAL NAG SIA GAL B:5;
C:5;
Valid;
Valid;
none;
none;
submit data
997.88 n/a O=C([...
EDO A:5;
A:6;
C:291;
D:290;
E:290;
E:4;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GOL A:4;
B:290;
C:290;
D:2;
E:3;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X17 1.75 Å NON-ENZYME: OTHER JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GD1B OLIGOSACCHARI JC POLYOMAVIRUS BETA-SANDWICH JELLY-ROLL VIRAL MAJOR CAPSID PROTEIN GLYCAPROTEIN
Ref.: THE GREATER AFFINITY OF JC POLYOMAVIRUS CAPSID FOR 2,6-LINKED LACTOSERIES TETRASACCHARIDE C THAN FOR O SIALYLATED GLYCANS IS A MAJOR DETERMINANT OF INFECT J.VIROL. V. 89 6364 2015
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3NXD - BGC GAL NAG SIA GAL n/a n/a
2 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
3 4X15 - SIA GAL BGC NGA n/a n/a
4 4X10 - SIA GAL BGC NGA n/a n/a
5 4X0Z - SIA GAL BGC NGA GAL n/a n/a
6 4X17 - SIA SIA n/a n/a
7 4JCF - SIA GAL NAG n/a n/a
8 4X12 - SIA SIA n/a n/a
9 4X14 - SIA GAL BGC NGA GAL n/a n/a
10 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
11 4X13 - SIA GAL NAG GAL BGC n/a n/a
70% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 families.
1 5CPZ - SIA SIA GAL NGA GAL n/a n/a
2 5CPW - SIA SIA GAL NGA GAL n/a n/a
3 5CQ0 - SIA GAL NGA GAL n/a n/a
4 5CPY - SIA GAL NGA GAL n/a n/a
5 1VPS - SIA GAL NAG SIA n/a n/a
6 5CPX - SIA GAL n/a n/a
7 4U60 - SIA GAL BGC NGA GAL n/a n/a
8 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
9 4U61 - GAL SIA n/a n/a
10 4POR - BGC SIA GAL n/a n/a
11 4POS - NAG SIA GAL n/a n/a
12 4POT - NAG GAL NGC n/a n/a
13 4MJ0 - BGC SIA SIA GAL n/a n/a
14 3NXD - BGC GAL NAG SIA GAL n/a n/a
15 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
16 4X15 - SIA GAL BGC NGA n/a n/a
17 4X10 - SIA GAL BGC NGA n/a n/a
18 4X0Z - SIA GAL BGC NGA GAL n/a n/a
19 4JCF - SIA GAL NAG n/a n/a
20 4X12 - SIA SIA n/a n/a
21 4X14 - SIA GAL BGC NGA GAL n/a n/a
22 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
23 4X13 - SIA GAL NAG GAL BGC n/a n/a
24 4MBY - SIA GAL n/a n/a
25 4MBZ - SIA GAL n/a n/a
26 4FMI - NAG SIA GAL n/a n/a
27 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
28 4FMH - SIA GAL n/a n/a
50% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 5CPZ - SIA SIA GAL NGA GAL n/a n/a
2 5CPW - SIA SIA GAL NGA GAL n/a n/a
3 5CQ0 - SIA GAL NGA GAL n/a n/a
4 5CPY - SIA GAL NGA GAL n/a n/a
5 1VPS - SIA GAL NAG SIA n/a n/a
6 5CPX - SIA GAL n/a n/a
7 4U60 - SIA GAL BGC NGA GAL n/a n/a
8 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
9 4U61 - GAL SIA n/a n/a
10 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
11 4POR - BGC SIA GAL n/a n/a
12 4POS - NAG SIA GAL n/a n/a
13 4POT - NAG GAL NGC n/a n/a
14 4MJ0 - BGC SIA SIA GAL n/a n/a
15 3NXD - BGC GAL NAG SIA GAL n/a n/a
16 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
17 4X15 - SIA GAL BGC NGA n/a n/a
18 4X10 - SIA GAL BGC NGA n/a n/a
19 4X0Z - SIA GAL BGC NGA GAL n/a n/a
20 4X17 - SIA SIA n/a n/a
21 4JCF - SIA GAL NAG n/a n/a
22 4X12 - SIA SIA n/a n/a
23 4X14 - SIA GAL BGC NGA GAL n/a n/a
24 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
25 4X13 - SIA GAL NAG GAL BGC n/a n/a
26 4MBY - SIA GAL n/a n/a
27 4MBZ - SIA GAL n/a n/a
28 4FMI - NAG SIA GAL n/a n/a
29 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
30 4FMH - SIA GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BGC GAL NAG SIA GAL; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL NAG GAL GLC 1 1
2 BGC GAL NAG SIA GAL 1 1
3 SIA GAL NAG GAL BGC 1 1
4 GAL NAG SIA GAL 0.839286 1
5 SIA GAL NAG GAL 0.839286 1
6 NAG GAL SIA 0.734513 1
7 4U0 0.695652 0.943396
8 SIA NAG GAL GAL 0.669421 1
9 GAL BGC SIA 0.65812 0.943396
10 GLA GLC SIA 0.65812 0.943396
11 BGC GAL SIA 0.65812 0.943396
12 SIA BGC GAL 0.65812 0.943396
13 SIA GAL BGC 0.65812 0.943396
14 BGC SIA GAL 0.65812 0.943396
15 SIA GAL GLC 0.65812 0.943396
16 GAL NGA SIA GAL BGC 0.630769 0.981132
17 SIA GAL BGC NGA GAL 0.630769 0.981132
18 GAL NGA GAL BGC SIA 0.630769 0.981132
19 BGC GAL SIA NGA GAL 0.630769 0.981132
20 GAL NGA GAL SIA 0.629032 0.981132
21 SIA GAL NGA GAL 0.629032 0.981132
22 4U1 0.619835 0.981132
23 GAL BGC SIA NGA 0.617188 0.981132
24 SIA GAL BGC NGA 0.617188 0.981132
25 BGC GAL SIA NGA 0.617188 0.981132
26 SLT 0.613445 0.924528
27 GAL SIA 0.609091 0.962264
28 GLC GAL NAG GAL 0.605505 0.849057
29 BGC GAL SIA SIA GAL NGA 0.598485 0.981132
30 GAL BGC GAL SIA NGA SIA 0.598485 0.981132
31 MN0 GAL GLC 0.593496 0.907407
32 SIA NAG GAL 0.58871 0.963636
33 BGC SIA SIA GAL 0.587786 0.962963
34 SIA SIA GLA BGC 0.587786 0.962963
35 SIA GAL NAG SIA 0.585938 1
36 GAL TNR SIA 0.578125 0.981481
37 NAG SIA GAL 0.577236 0.981132
38 SIA GAL NAG 0.577236 0.981132
39 SIA SIA GAL NGA GAL 0.565217 0.962963
40 NAG GAL NGC 0.55814 0.944444
41 SIA GAL SIA GLC NGA 0.556338 0.962963
42 SIA GAL SIA BGC NGA 0.556338 0.962963
43 GAL SIA NGA GAL 0.553846 0.981132
44 SIA GAL NDG SIA 0.549618 0.963636
45 BGC GAL SIA NGA GAL SIA 0.544218 0.83871
46 4U2 0.536 0.962264
47 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.531034 0.981481
48 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.531034 0.981481
49 GAL SIA NGA GAL SIA 0.530303 0.981132
50 NAG GAL GAL NAG GAL 0.526316 0.90566
51 SIA GAL NGA 0.523438 0.981132
52 SIA GAL NGS 0.522388 0.8
53 NGA GLA GAL BGC 0.517241 0.849057
54 NAG GAL BGC 0.513274 0.849057
55 GAL NAG GAL NAG GAL NAG 0.513043 0.924528
56 NAG GAL GAL NAG 0.513043 0.90566
57 NGA GAL SIA 0.507812 0.981132
58 SIA GAL A2G 0.507812 0.981132
59 LAT NAG GAL 0.504348 0.849057
60 GAL NAG GAL BGC 0.504348 0.849057
61 BGC GAL NAG GAL 0.504348 0.849057
62 NAG FUC SIA GAL 0.50365 0.981132
63 FUC NDG GAL SIA 0.50365 0.981132
64 NDG FUC SIA GAL 0.50365 0.981132
65 SIA GAL NDG FUC 0.50365 0.981132
66 SIA GAL NAG FUC 0.50365 0.981132
67 SIA GLA NAG FUC 0.50365 0.981132
68 GAL NGA GLA BGC GAL 0.5 0.849057
69 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.496644 0.981481
70 FUC BGC GAL NAG GAL 0.496 0.867925
71 SIA SIA GAL NGA GAL SIA 0.482759 0.962963
72 SIA GLA NGS FUC 0.479452 0.8
73 SIA GAL MAG FUC 0.471429 0.944444
74 SIA GAL 0.471074 0.943396
75 SIA GAL BGC 16C 0.462025 0.854839
76 NAG NAG BMA MAN MAN 0.460938 0.90566
77 MAN MAN NAG MAN NAG 0.460938 0.90566
78 SIA NAG 0.459677 0.928571
79 NAG NAG BMA MAN 0.456 0.909091
80 FUC GAL NAG GAL BGC 0.453125 0.867925
81 NGC GAL NGA POL AZI 0.452055 0.772727
82 NAG MAN GAL BMA NAG MAN NAG GAL 0.451128 0.924528
83 NAG MAN GAL BMA NDG MAN NAG GAL 0.451128 0.924528
84 MAN BMA NAG NAG MAN NAG GAL GAL 0.451128 0.924528
85 NAG MAN MAN MAN NAG GAL NAG GAL 0.451128 0.924528
86 BGC GAL CEQ SLB NGA GAL SIA SIA 0.450617 0.852459
87 BGC GAL NAG GAL FUC FUC 0.450382 0.886792
88 GLC GAL NAG GAL FUC FUC 0.450382 0.886792
89 SIA 2FG NAG 0.448529 0.912281
90 GAL NAG MAN 0.448276 0.849057
91 MAN NAG GAL 0.448276 0.849057
92 SIA 2FG 0.448 0.877193
93 BGC 18C GAL SIA 0.447205 0.854839
94 GLC GAL NAG GAL FUC A2G 0.441176 0.924528
95 A2G GAL NAG FUC GAL GLC 0.441176 0.924528
96 NAG GAL NAG 0.436975 0.90566
97 BGC 18C GAL NGA SIA GAL 0.436782 0.854839
98 GLA GAL NAG FUC GAL GLC 0.43609 0.867925
99 NAG MAN BMA NDG MAN NAG GAL 0.434783 0.924528
100 GAL NAG GAL 0.433333 0.886792
101 GLA GAL NAG 0.431034 0.849057
102 NAG GAL GAL 0.431034 0.849057
103 MAN BMA NAG 0.431034 0.849057
104 NGC MBG 0.429688 0.890909
105 NAG MAN GAL MAN MAN NAG GAL 0.427481 0.90566
106 NGA GAL BGC 0.42735 0.849057
107 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.425532 0.90566
108 SIA SIA GAL 0.422222 0.962963
109 GLA GAL BGC 0.418182 0.622642
110 GLA GAL GAL 0.418182 0.622642
111 BGC BGC BGC BGC 0.415929 0.622642
112 SIA CMO 0.415929 0.854545
113 BGC BGC BGC BGC BGC BGC BGC BGC 0.415929 0.622642
114 A2G THR ALA PRO GLY GLY NAG SIA 0.413408 0.779412
115 5N6 GAL 0.412214 0.944444
116 NAG NAG BMA MAN MAN MAN MAN 0.409722 0.909091
117 SIA GAL SIA BGC NGA CEQ 0.409639 0.815385
118 Z3Q GAL 5N6 0.409396 0.825397
119 NAG BMA NAG MAN MAN NAG NAG 0.405797 0.924528
120 FUC BGC GAL NAG 0.403101 0.867925
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4X17; Ligand: SIA; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 4x17.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A89 ADP 0.03814 0.40176 1.28205
2 5A89 FMN 0.03814 0.40176 1.28205
3 5BVE 4VG 0.03605 0.41399 2.94118
4 4M1U A2G MBG 0.0001158 0.40463 4.28571
5 1NB9 RBF 0.02795 0.40495 5.44218
6 1NB9 ADP 0.02795 0.40495 5.44218
7 1M5B BN1 0.03077 0.43579 5.70342
8 4IPH 1FJ 0.008427 0.41579 6.50407
Pocket No.: 2; Query (leader) PDB : 4X17; Ligand: SIA SIA; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 4x17.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A89 ADP 0.02618 0.41345 1.28205
2 5A89 FMN 0.02618 0.41345 1.28205
3 1XSE NDP 0.0373 0.40462 2.57353
4 5BVE 4VG 0.03791 0.41605 2.94118
5 4M1U A2G MBG 0.0001014 0.41353 4.28571
6 4M1U MBG A2G 0.01451 0.4068 4.28571
7 1NB9 RBF 0.01984 0.41591 5.44218
8 1NB9 ADP 0.01984 0.41591 5.44218
9 4IPH 1FJ 0.012 0.41231 6.50407
10 1S4M LUM 0.01621 0.40877 9.19118
11 1BB6 UMG 0.01297 0.40423 14.7287
Pocket No.: 3; Query (leader) PDB : 4X17; Ligand: SIA SIA; Similar sites found: 17
This union binding pocket(no: 3) in the query (biounit: 4x17.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3I59 N6S 0.007376 0.4228 2.00803
2 1KPG SAH 0.02338 0.40281 2.57353
3 1KPH SAH 0.02365 0.40255 2.57353
4 4FWE FAD 0.04449 0.41002 3.30882
5 1NF3 GNP 0.0235 0.40566 3.58974
6 1QD1 FON 0.02351 0.40566 3.67647
7 1CX4 CMP 0.0132 0.40836 4.41176
8 3UN3 G16 0.02151 0.40306 4.41176
9 2HRL SIA GAL SIA BGC NGA CEQ 0.004314 0.42044 4.72441
10 1M5B BN1 0.009909 0.47522 5.70342
11 1N07 FMN 0.02594 0.41223 6.13497
12 1VYF OLA 0.006336 0.4331 6.66667
13 3ZW2 GLA NAG GAL FUC 0.01228 0.40992 6.89655
14 3ZW2 NAG GAL FUC 0.01242 0.40105 6.89655
15 1U7Z PMT 0.03144 0.40891 7.9646
16 1ZB6 GST 0.03293 0.40331 10.2941
17 4HP0 NOJ NAG NAG NAG 0.008124 0.43214 15.5039
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