Receptor
PDB id Resolution Class Description Source Keywords
4X14 2.3 Å NON-ENZYME: OTHER JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GM1 OLIGOSACCHARID 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:306;
D:308;
D:307;
E:302;
E:303;
B:307;
C:307;
C:308;
A:304;
B:308;
A:303;
A:302;
A:305;
E:304;
C:309;
 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 A:301;
B:305;
D:306;
C:306;
E:301;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
K A:306;
A:307;
D:309;
B:309;
C:310;
 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 SIA NGA GAL G:1;
H:1;
 Valid;
Valid;
 none;
none;
 submit data
997.88 n/a O=C(N...
SIA GAL NGA GAL F:4;
 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 SIA NGA GAL; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA NGA GAL 1 1
2 BGC GAL SIA NGA GAL SIA 0.917431 1
3 BGC GAL SIA NGA GAL FUC 0.841667 1
4 SIA GAL NGA GAL 0.834862 1
5 BGC GAL SIA NAG 0.830357 1
6 GAL NGA GAL SIA 0.818182 1
7 BGC GAL GLA NGA GAL SIA 0.794872 1
8 GAL SIA NGA GAL SIA 0.769912 1
9 BGC GAL SIA NGA SIA 0.738095 0.981132
10 GAL NGA GAL SIA SIA 0.725806 0.981132
11 GAL SIA NGA GAL 0.724138 0.981132
12 GAL SIA NGA GAL SIA SIA 0.690476 0.981132
13 BGC GAL SIA SIA 0.674797 0.981132
14 GAL SIA NGA 0.663793 1
15 GLC GAL NGC 0.65812 0.924528
16 BGC CEQ GAL SLB NGA GAL SIA SIA 0.652482 0.83871
17 BGC GAL SIA 0.649573 0.943396
18 BGC 18C GAL SIA NGA GAL 0.642384 0.83871
19 NAG GAL SIA 0.641026 1
20 A2G GAL SIA 0.632479 1
21 BGC GAL NAG GAL SIA 0.630769 0.981132
22 GAL NAG FUC GAL SIA 0.603053 1
23 GAL NAG GAL SIA 0.6 0.981132
24 NAG GAL NGC 0.592 0.962264
25 NAG GAL SIA SIA 0.582677 0.981132
26 NAG FUC GAL SIA 0.581395 1
27 MAG FUC GAL SIA 0.581395 0.962264
28 NGS GAL SIA 0.578125 0.787879
29 NGA GAL SIA 0.576 0.980769
30 NDG GAL SIA SIA 0.55814 0.945455
31 BGC GAL NAG GAL 0.554545 0.865385
32 NAG GAL NAG GAL SIA 0.551471 0.981132
33 BGC GAL NGA GAL 0.550459 0.865385
34 BGC GAL GLA NGA GAL 0.548673 0.865385
35 NAG 2FG SIA 0.547619 0.928571
36 NGA POL GAL NGC AZI 0.532847 0.784615
37 2FG SIA 0.529915 0.892857
38 NGS FUC GLA SIA 0.528571 0.787879
39 CEQ BGC NGA GAL SIA SIA 0.526316 0.8
40 NAG GAL PKM 0.523077 0.981132
41 Z3Q GAL 5N6 0.518248 0.83871
42 BGC 16C GAL SIA 0.506579 0.83871
43 GAL 5N6 0.5 0.962264
44 NAG GAL 5N6 0.5 0.962963
45 GAL SIA SIA 0.496063 0.981132
46 BGC 18C GAL SIA 0.490323 0.83871
47 MBG NGC 0.483607 0.907407
48 BGC GAL NAG GAL FUC 0.472 0.884615
49 GLC GAL NAG GAL FUC GLA 0.465116 0.884615
50 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.456954 0.945455
51 C4W NAG FUC BMA MAN NAG GAL SIA 0.450617 0.852459
52 BGC GAL GLA NGA 0.45 0.865385
53 BGC GAL NAG GAL FUC FUC 0.446154 0.903846
54 BGC GAL NAG 0.444444 0.865385
55 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.44186 0.852459
56 GAL SIA 0.429752 0.924528
57 GLC GAL NAG GAL FUC A2G 0.426471 0.942308
58 SIA CMO 0.423423 0.87037
59 BGC GAL NGA 0.422414 0.865385
60 BGC GAL NAG NAG GAL GAL 0.412214 0.923077
61 BGC GAL GLA 0.4 0.634615
Ligand no: 2; Ligand: SIA GAL NGA GAL; Similar ligands found: 69
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL NGA GAL 1 1
2 GAL SIA NGA GAL SIA 0.881188 1
3 BGC GAL SIA NGA GAL 0.834862 1
4 GAL SIA NGA 0.794118 1
5 GAL SIA NGA GAL 0.792453 0.981132
6 GAL SIA NGA GAL SIA SIA 0.780702 0.981132
7 BGC GAL SIA NGA GAL SIA 0.761062 1
8 GAL NGA GAL SIA 0.743119 1
9 BGC GAL GLA NGA GAL SIA 0.709402 1
10 BGC GAL SIA NGA GAL FUC 0.701613 1
11 BGC GAL SIA NAG 0.681035 1
12 GAL NGA GAL SIA SIA 0.672131 0.981132
13 GAL NAG GAL SIA 0.666667 0.981132
14 A2G GAL SIA 0.66055 1
15 GAL NAG FUC GAL SIA 0.626016 1
16 NAG GAL SIA 0.625 1
17 BGC GAL SIA NGA SIA 0.620155 0.981132
18 NAG FUC GAL SIA 0.616667 1
19 BGC GAL SIA SIA 0.606557 0.981132
20 NAG GAL SIA SIA 0.605042 0.981132
21 BGC CEQ GAL SLB NGA GAL SIA SIA 0.604317 0.83871
22 NGA GAL SIA 0.598291 0.980769
23 NAG 2FG SIA 0.594828 0.928571
24 BGC GAL SIA 0.591304 0.943396
25 MAG FUC GAL SIA 0.590164 0.962264
26 BGC 18C GAL SIA NGA GAL 0.586667 0.83871
27 2FG SIA 0.579439 0.892857
28 NAG GAL NGC 0.575 0.962264
29 GLC GAL NGC 0.57265 0.924528
30 NDG GAL SIA SIA 0.565574 0.945455
31 GAL SIA SIA 0.565217 0.981132
32 NGS GAL SIA 0.560976 0.787879
33 BGC GAL NAG GAL SIA 0.553846 0.981132
34 NGA POL GAL NGC AZI 0.550388 0.784615
35 NGS FUC GLA SIA 0.545455 0.787879
36 GAL 5N6 0.544643 0.962264
37 NAG GAL NAG GAL SIA 0.534351 0.981132
38 Z3Q GAL 5N6 0.523077 0.83871
39 MBG NGC 0.513274 0.907407
40 NAG GAL PKM 0.504 0.981132
41 NAG GAL 5N6 0.492188 0.962963
42 BGC GAL NGA GAL 0.485981 0.865385
43 CEQ BGC NGA GAL SIA SIA 0.48 0.8
44 BGC 16C GAL SIA 0.47973 0.83871
45 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.478873 0.945455
46 BGC 18C GAL SIA 0.473333 0.83871
47 GAL SIA 0.468468 0.924528
48 SIA CMO 0.465347 0.87037
49 BGC GAL NAG GAL 0.463636 0.865385
50 BGC GAL GLA NGA GAL 0.460177 0.865385
51 C4W NAG FUC BMA MAN NAG GAL SIA 0.433121 0.852459
52 WIA SIA 0.432203 0.894737
53 NAG SIA 0.432203 0.910714
54 MNA 0.427184 0.851852
55 A2G SER GAL 0.423423 0.907407
56 SIA SIA 0.422414 0.962264
57 MGC GAL 0.421569 0.867925
58 A2G THR GAL 0.419643 0.943396
59 SLB SIA SIA SIA 0.418803 0.962264
60 SLB SIA SIA 0.418803 0.962264
61 SLB SIA SIA SIA SIA 0.418803 0.962264
62 SIA SIA SIA SIA SIA SIA SIA 0.418803 0.962264
63 SIA SIA SIA 0.413223 0.962264
64 GAL NAG FUC GAL 0.410256 0.884615
65 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.408284 0.852459
66 A2G GAL 0.407767 0.865385
67 GAL NAG GAL 0.401786 0.865385
68 BGC FUC GAL NAG GAL 0.4 0.884615
69 GAL NGA A2G 0.4 0.923077
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL SIA NGA GAL; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: SIA GAL NGA GAL; 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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