Receptor
PDB id Resolution Class Description Source Keywords
4x13 2 Å NON-ENZYME: OTHER JC POLYOMAVIRUS GENOTYPE 3 VP1 IN COMPLEX WITH LSTC PENTASAC JC POLYOMAVIRUS TYPE 3 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:306;
B:313;
B:307;
B:309;
C:307;
A:304;
B:310;
A:303;
E:308;
E:306;
E:309;
B:308;
A:302;
D:303;
E:307;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
GOL D:301;
B:311;
D:302;
A:301;
D:304;
B:312;
A:305;
E:305;
C:309;
C:308;
C:306;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
K E:310;
A:306;
C:310;
D:305;
B:314;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
 submit data
39.098 K [K+]
BGC GAL NAG GAL SIA G:1;
F:1;
 Valid;
Valid;
 none;
none;
 submit data
997.88 n/a O=C(N...
GAL NAG GAL SIA H:1;
 Valid;
 none;
 submit data
835.739 n/a O=C(N...
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 1610 families.
1 3NXD - BGC GAL NAG GAL SIA n/a n/a
2 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
3 4X15 - BGC GAL SIA NGA n/a n/a
4 4X10 - GAL SIA NGA n/a n/a
5 4X0Z - BGC GAL SIA NGA GAL n/a n/a
6 4X17 - SIA SIA n/a n/a
7 4JCF - NAG GAL SIA n/a n/a
8 4X12 - SIA SIA n/a n/a
9 4X14 - BGC GAL SIA NGA GAL n/a n/a
10 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
11 4X13 - BGC GAL NAG GAL SIA n/a n/a
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 5CPZ - GAL NGA GAL SIA SIA n/a n/a
2 5CPW - GAL SIA NGA GAL SIA SIA n/a n/a
3 5CQ0 - GAL NGA GAL SIA n/a n/a
4 5CPY - GAL NGA GAL SIA n/a n/a
5 1VPS - NAG GAL SIA SIA n/a n/a
6 5CPX - NAG GAL SIA n/a n/a
7 4U60 - BGC GAL SIA NGA GAL n/a n/a
8 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
9 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
10 4U61 - GAL SIA n/a n/a
11 6HKU - GLC GAL SIA n/a n/a
12 4POR - BGC GAL SIA n/a n/a
13 4POS - NAG GAL SIA n/a n/a
14 4POT - NAG GAL NGC n/a n/a
15 4MJ0 - SIA SIA n/a n/a
16 3NXD - BGC GAL NAG GAL SIA n/a n/a
17 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
18 4X15 - BGC GAL SIA NGA n/a n/a
19 4X10 - GAL SIA NGA n/a n/a
20 4X0Z - BGC GAL SIA NGA GAL n/a n/a
21 4X17 - SIA SIA n/a n/a
22 4JCF - NAG GAL SIA n/a n/a
23 4X12 - SIA SIA n/a n/a
24 4X14 - BGC GAL SIA NGA GAL n/a n/a
25 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
26 4X13 - BGC GAL NAG GAL SIA n/a n/a
27 4MBY - GAL SIA n/a n/a
28 4MBZ - GAL SIA n/a n/a
29 4FMI - NAG GAL SIA n/a n/a
30 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
31 4FMH - GAL SIA n/a n/a
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 5CPZ - GAL NGA GAL SIA SIA n/a n/a
2 5CPW - GAL SIA NGA GAL SIA SIA n/a n/a
3 5CQ0 - GAL NGA GAL SIA n/a n/a
4 5CPY - GAL NGA GAL SIA n/a n/a
5 1VPS - NAG GAL SIA SIA n/a n/a
6 5CPX - NAG GAL SIA n/a n/a
7 4U60 - BGC GAL SIA NGA GAL n/a n/a
8 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
9 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
10 4U61 - GAL SIA n/a n/a
11 6HKU - GLC GAL SIA n/a n/a
12 3BWR Kd ~ 3 mM BGC GAL SIA NGA GAL n/a n/a
13 4POR - BGC GAL SIA n/a n/a
14 4POS - NAG GAL SIA n/a n/a
15 4POT - NAG GAL NGC n/a n/a
16 6Y5Y - BGC GAL SIA n/a n/a
17 4MJ0 - SIA SIA n/a n/a
18 6Y64 - GAL SIA n/a n/a
19 3NXD - BGC GAL NAG GAL SIA n/a n/a
20 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
21 4X15 - BGC GAL SIA NGA n/a n/a
22 4X10 - GAL SIA NGA n/a n/a
23 4X0Z - BGC GAL SIA NGA GAL n/a n/a
24 4X17 - SIA SIA n/a n/a
25 4JCF - NAG GAL SIA n/a n/a
26 4X12 - SIA SIA n/a n/a
27 4X14 - BGC GAL SIA NGA GAL n/a n/a
28 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
29 4X13 - BGC GAL NAG GAL SIA n/a n/a
30 4MBY - GAL SIA n/a n/a
31 4MBZ - GAL SIA n/a n/a
32 4FMI - NAG GAL SIA n/a n/a
33 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
34 4FMH - GAL SIA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC GAL NAG GAL SIA; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL NAG GAL SIA 1 1
2 NAG GAL NAG GAL SIA 0.884956 1
3 BGC GAL SIA 0.82243 0.962264
4 BGC GAL GLA NGA GAL SIA 0.68254 0.981132
5 GAL NAG GAL SIA 0.669421 1
6 NAG GAL 5N6 0.650406 0.981481
7 BGC GAL SIA NGA GAL 0.630769 0.981132
8 GAL NGA GAL SIA 0.629032 0.981132
9 BGC GAL SIA NAG 0.617188 0.981132
10 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.602564 0.868852
11 BGC GAL SIA NGA GAL SIA 0.598485 0.981132
12 GLC GAL NGC 0.593496 0.907407
13 C4W NAG FUC BMA MAN NAG GAL SIA 0.590604 0.868852
14 BGC GAL SIA SIA 0.587786 0.962963
15 NAG GAL SIA SIA 0.585938 1
16 NAG GAL SIA 0.577236 0.981132
17 BGC GAL SIA NGA GAL FUC 0.570423 0.981132
18 GAL NGA GAL SIA SIA 0.565217 0.962963
19 BGC GAL NAG NAG GAL GAL 0.558333 0.90566
20 NAG GAL NGC 0.55814 0.944444
21 BGC GAL SIA NGA SIA 0.556338 0.962963
22 SIA GAL NGA GAL 0.553846 0.981132
23 NDG GAL SIA SIA 0.549618 0.963636
24 NGS GAL SIA 0.533835 0.776119
25 GAL SIA NGA GAL SIA 0.530303 0.981132
26 GAL NAG GAL NAG GAL 0.526316 0.90566
27 GAL NAG FUC GAL SIA 0.52518 0.981132
28 GAL SIA NGA 0.523438 0.981132
29 BGC GAL GLA NGA 0.517241 0.849057
30 BGC GAL NAG 0.513274 0.849057
31 NAG GAL NAG GAL NAG GAL 0.513043 0.924528
32 NAG GAL NAG GAL 0.513043 0.90566
33 GAL SIA 0.508621 0.943396
34 A2G GAL SIA 0.507812 0.981132
35 GAL SIA NGA GAL 0.507463 1
36 BGC GAL NAG GAL 0.504348 0.849057
37 NAG FUC GAL SIA 0.50365 0.981132
38 BGC GAL GLA NGA GAL 0.5 0.849057
39 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.5 0.963636
40 BGC FUC GAL NAG GAL 0.496 0.867925
41 NAG GAL PKM 0.492537 0.962963
42 NGS FUC GLA SIA 0.489655 0.776119
43 GAL SIA NGA GAL SIA SIA 0.482759 0.962963
44 GAL NAG GAL 0.482456 0.849057
45 NGA GAL SIA 0.474074 0.962264
46 MAG FUC GAL SIA 0.471429 0.944444
47 BGC 16C GAL SIA 0.462025 0.854839
48 NAG NAG MAN MAN MAN 0.460938 0.90566
49 NAG SIA 0.459677 0.928571
50 NAG NAG BMA MAN 0.456 0.909091
51 BGC GAL NAG GAL FUC 0.453125 0.867925
52 NGA POL GAL NGC AZI 0.452055 0.772727
53 NAG BMA MAN MAN NAG GAL NAG GAL 0.451128 0.924528
54 BGC GAL NAG GAL FUC FUC 0.450382 0.886792
55 NAG 2FG SIA 0.448529 0.912281
56 MAN NAG GAL 0.448276 0.849057
57 2FG SIA 0.448 0.877193
58 BGC 18C GAL SIA 0.447205 0.854839
59 BGC CEQ GAL SLB NGA GAL SIA SIA 0.441718 0.825397
60 GLC GAL NAG GAL FUC A2G 0.441176 0.924528
61 NAG NAG BMA MAN NAG 0.4375 0.924528
62 NAG GAL NAG 0.436975 0.90566
63 BGC GAL NGA GAL 0.436975 0.849057
64 BGC 18C GAL SIA NGA GAL 0.436782 0.854839
65 GLC GAL NAG GAL FUC GLA 0.43609 0.867925
66 NDG BMA MAN MAN NAG GAL NAG 0.434783 0.924528
67 NAG NAG BMA MAN MAN NAG GAL NAG 0.431655 0.924528
68 NAG GAL GAL 0.431034 0.849057
69 MBG NGC 0.429688 0.890909
70 BGC GAL NGA 0.42735 0.849057
71 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.425532 0.90566
72 GAL SIA SIA 0.422222 0.962963
73 A2G THR ALA PRO GLY GLY NAG SIA 0.421348 0.768116
74 C4W NAG FUC BMA MAN 0.42029 0.909091
75 BGC GAL GLA 0.418182 0.622642
76 BGC BGC BGC BGC BGC BGC BGC BGC 0.415929 0.622642
77 SIA CMO 0.415929 0.854545
78 GAL 5N6 0.412214 0.944444
79 BMA MAN MAN NAG GAL NAG 0.411765 0.90566
80 NAG NAG BMA MAN MAN MAN MAN 0.409722 0.909091
81 CEQ BGC NGA GAL SIA SIA 0.409639 0.815385
82 Z3Q GAL 5N6 0.409396 0.825397
83 BGC FUC GAL NAG 0.403101 0.867925
84 NAG NAG FUL BMA MAN MAN NAG GAL 0.402685 0.927273
Ligand no: 2; Ligand: GAL NAG GAL SIA; Similar ligands found: 72
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL NAG GAL SIA 1 1
2 BGC GAL SIA 0.694444 0.962264
3 BGC GAL NAG GAL SIA 0.669421 1
4 SIA GAL NGA GAL 0.666667 0.981132
5 NAG GAL NAG GAL SIA 0.661157 1
6 NAG GAL SIA SIA 0.646552 1
7 GAL SIA NGA GAL 0.623932 1
8 BGC GAL SIA NGA GAL 0.6 0.981132
9 GAL NAG FUC GAL SIA 0.6 0.981132
10 BGC GAL GLA NGA GAL SIA 0.6 0.981132
11 NAG GAL 5N6 0.591667 0.981481
12 GAL NGA GAL SIA 0.583333 0.981132
13 GAL SIA NGA GAL SIA 0.583333 0.981132
14 GAL SIA 0.567308 0.943396
15 NDG GAL SIA SIA 0.565574 0.963636
16 A2G GAL SIA 0.560345 0.981132
17 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.555556 0.963636
18 BGC GAL SIA NGA GAL SIA 0.542636 0.981132
19 GAL SIA NGA 0.537815 0.981132
20 GAL SIA NGA GAL SIA SIA 0.526316 0.962963
21 NGS GAL SIA 0.52381 0.776119
22 NAG SIA 0.522523 0.928571
23 GAL NGA GAL SIA SIA 0.522388 0.962963
24 NAG GAL SIA 0.516667 0.981132
25 2FG SIA 0.508929 0.877193
26 NGA GAL SIA 0.508065 0.962264
27 BGC GAL SIA NGA GAL FUC 0.507143 0.981132
28 NAG 2FG SIA 0.504065 0.912281
29 GAL SIA SIA 0.5 0.962963
30 BGC GAL SIA NAG 0.5 0.981132
31 C4W NAG FUC BMA MAN NAG GAL SIA 0.5 0.868852
32 NGS FUC GLA SIA 0.5 0.776119
33 NAG FUC GAL SIA 0.492308 0.981132
34 GAL 5N6 0.491379 0.944444
35 BGC GAL SIA SIA 0.484848 0.962963
36 GAL NAG GAL 0.481132 0.849057
37 MAG FUC GAL SIA 0.480916 0.944444
38 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.478261 0.868852
39 NAG GAL NGC 0.476562 0.944444
40 GAL NAG FUC GAL 0.473214 0.867925
41 SIA CMO 0.465347 0.854545
42 A2G THR ALA PRO GLY GLY NAG SIA 0.460606 0.768116
43 GLC GAL NGC 0.460317 0.907407
44 NGA POL GAL NGC AZI 0.459854 0.772727
45 GAL NAG GAL NAG GAL 0.459459 0.90566
46 GAL NGA A2G 0.45283 0.90566
47 BGC GAL SIA NGA SIA 0.451389 0.962963
48 BGC 18C GAL SIA NGA GAL 0.451219 0.854839
49 MNA 0.441176 0.836364
50 BGC CEQ GAL SLB NGA GAL SIA SIA 0.43871 0.825397
51 BGC GAL NAG GAL 0.4375 0.849057
52 MBG NGC 0.436975 0.890909
53 Z3Q GAL 5N6 0.434783 0.825397
54 BGC GAL GLA NGA GAL 0.434783 0.849057
55 GLA NAG GAL FUC 0.434783 0.867925
56 NAG GAL PKM 0.424242 0.962963
57 WIA SIA 0.420168 0.912281
58 BGC GAL NGA GAL 0.419643 0.849057
59 BGC 16C GAL SIA 0.412903 0.854839
60 BMA MAN NAG 0.410714 0.849057
61 SIA SIA 0.410256 0.944444
62 1GN ACY GAL 1GN BGC ACY GAL BGC 0.409836 0.90566
63 GAL NAG GAL FUC FUC 0.408333 0.886792
64 A2G GAL 0.407767 0.849057
65 BGC 18C GAL SIA 0.407643 0.854839
66 SIA SIA SIA SIA SIA SIA SIA 0.40678 0.944444
67 SLB SIA SIA 0.40678 0.944444
68 SLB SIA SIA SIA 0.40678 0.944444
69 SLB SIA SIA SIA SIA 0.40678 0.944444
70 GAL GLA 0.40625 0.622642
71 SIA SIA SIA 0.401639 0.944444
72 GLY PRO ALA THR PRO ALA PRO A2G SIA 0.4 0.768116
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL NAG GAL SIA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: GAL NAG GAL SIA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4X17; Ligand: SIA SIA; 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: 4x17.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4X17; Ligand: SIA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4x17.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4X17; Ligand: SIA SIA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4x17.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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