Receptor
PDB id Resolution Class Description Source Keywords
4x10 1.9 Å NON-ENZYME: OTHER JC POLYOMAVIRUS GENOTYPE 3 VP1 IN COMPLEX WITH GM2 OLIGOSACC JC POLYOMAVIRUS TYPE 3 BETA-SANDWICH JELLY-ROLL VIRAL CAPSID PROTEIN GLYCAN VIRPROTEIN
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
GOL D:305;
E:303;
A:301;
D:304;
B:306;
B:305;
A:302;
C:307;
B:309;
C:305;
D:306;
C:306;
E:301;
A:303;
B:308;
 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
92.094 C3 H8 O3 C(C(C...
EDO D:307;
E:302;
B:307;
C:308;
A:304;
E:304;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
K E:305;
A:306;
D:309;
C:309;
D:308;
B:310;
A:305;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
 submit data
39.098 K [K+]
GAL SIA NGA H:1;
 Valid;
 none;
 submit data
673.598 n/a O=C(N...
BGC GAL SIA NGA F:1;
G:1;
 Valid;
Valid;
 none;
none;
 submit data
n/a n/a
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: GAL SIA NGA; Similar ligands found: 77
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA NGA 1 1
2 BGC GAL SIA NAG 0.807692 1
3 SIA GAL NGA GAL 0.794118 1
4 GAL SIA NGA GAL SIA 0.759615 1
5 BGC GAL SIA NGA SIA 0.726496 0.981132
6 GAL SIA NGA GAL SIA SIA 0.675214 0.981132
7 BGC GAL SIA NGA GAL 0.663793 1
8 BGC GAL SIA NGA GAL SIA 0.641026 1
9 GAL SIA NGA GAL 0.619469 0.981132
10 GAL NGA GAL SIA 0.619469 1
11 BGC GAL SIA NGA GAL FUC 0.606299 1
12 NAG GAL SIA 0.605505 1
13 2FG SIA 0.60396 0.892857
14 A2G GAL SIA 0.59633 1
15 NAG 2FG SIA 0.589286 0.928571
16 GAL SIA SIA 0.587156 0.981132
17 NAG GAL NGC 0.582609 0.962264
18 BGC GAL GLA NGA GAL SIA 0.581967 1
19 BGC GAL SIA SIA 0.575 0.981132
20 NAG FUC GAL SIA 0.571429 1
21 GAL NAG FUC GAL SIA 0.569106 1
22 GLC GAL NGC 0.566372 0.924528
23 GAL NGA GAL SIA SIA 0.563492 0.981132
24 BGC GAL SIA 0.557522 0.943396
25 NGA GAL SIA 0.551724 0.980769
26 GAL 5N6 0.551402 0.962264
27 MBG NGC 0.54717 0.907407
28 NAG GAL SIA SIA 0.546219 0.981132
29 NGS GAL SIA 0.541667 0.787879
30 GAL NAG GAL SIA 0.537815 0.981132
31 NDG GAL SIA SIA 0.533333 0.945455
32 MAG FUC GAL SIA 0.532787 0.962264
33 BGC GAL NAG GAL SIA 0.523438 0.981132
34 BGC CEQ GAL SLB NGA GAL SIA SIA 0.51049 0.83871
35 NAG GAL NAG GAL SIA 0.503876 0.981132
36 NGS FUC GLA SIA 0.503817 0.787879
37 SIA CMO 0.5 0.87037
38 NGA POL GAL NGC AZI 0.496124 0.784615
39 CEQ BGC NGA GAL SIA SIA 0.493056 0.8
40 GAL SIA 0.485714 0.924528
41 NAG GAL PKM 0.483607 0.981132
42 AMU NAG 0.480769 0.961538
43 BGC 18C GAL SIA NGA GAL 0.471338 0.83871
44 BGC 16C GAL SIA 0.452055 0.83871
45 SIA SIA 0.449541 0.962264
46 NAG GAL 5N6 0.448819 0.962963
47 Z3Q GAL 5N6 0.44697 0.83871
48 BGC 18C GAL SIA 0.445946 0.83871
49 SLB SIA SIA SIA SIA 0.445455 0.962264
50 SIA SIA SIA SIA SIA SIA SIA 0.445455 0.962264
51 SLB SIA SIA 0.445455 0.962264
52 SLB SIA SIA SIA 0.445455 0.962264
53 C4W NAG FUC BMA MAN NAG GAL SIA 0.443709 0.852459
54 MNA 0.443299 0.851852
55 SIA SIA SIA 0.438596 0.962264
56 BGC GAL NGA 0.436893 0.865385
57 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.434783 0.852459
58 NAG SIA 0.433628 0.910714
59 WIA SIA 0.433628 0.894737
60 MAN NAG 0.43299 0.865385
61 GAL NGA 0.43 0.849057
62 GAL NGA A2G 0.427184 0.923077
63 BMA MAN NAG 0.424528 0.865385
64 GDL NAG 0.424242 0.923077
65 NAG NAG NAG NAG NAG NAG NAG NAG 0.421569 0.942308
66 NAG NAG NAG NAG NAG 0.421569 0.942308
67 NDG NAG NAG NAG NAG 0.421569 0.942308
68 NAG NAG NAG NAG NAG NAG 0.421569 0.942308
69 BGC FUC GAL NAG 0.421053 0.884615
70 AMV NAG AMU NAG 0.421053 0.943396
71 A2G THR ALA PRO GLY GLY NAG SIA 0.418182 0.753623
72 BGC FUC GAL FUC A2G 0.417391 0.903846
73 A2G NAG 0.41 0.923077
74 MAN MAN NAG 0.407407 0.867925
75 BGC GAL NAG 0.407407 0.865385
76 MBG A2G 0.405941 0.867925
77 BGC GAL GLA NGA 0.401786 0.865385
Ligand no: 2; Ligand: BGC GAL SIA NGA; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: GAL SIA NGA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: BGC GAL SIA NGA; Similar ligands found: 2
No: Ligand Similarity coefficient
1 BGC GAL SIA NGA 1.0000
2 BGC NGA GAL SIA 0.9853
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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