Receptor
PDB id Resolution Class Description Source Keywords
4X0Z 1.85 Å NON-ENZYME: OTHER JC POLYOMAVIRUS GENOTYPE 3 VP1 IN COMPLEX WITH GM1 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
EDO B:306;
D:309;
B:309;
D:311;
B:310;
E:305;
A:308;
A:305;
A:306;
C:310;
D:310;
E:304;
C:309;
 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;
 submit data
62.068 C2 H6 O2 C(CO)...
GOL D:308;
E:303;
D:307;
A:302;
C:307;
B:307;
A:304;
E:301;
B:308;
E:302;
C:311;
E:307;
A:301;
C:312;
E:306;
B:305;
A:307;
C:305;
D:306;
C:308;
C:306;
A:303;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
K E:308;
A:310;
C:314;
A:309;
B:311;
C:313;
B:312;
D:313;
D:312;
A:311;
 Part of Protein;
Part of Protein;
Part of Protein;
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;
none;
none;
none;
 submit data
39.098 K [K+]
BGC GAL SIA NGA GAL H:1;
 Valid;
 none;
 submit data
997.88 n/a O=C(N...
GAL SIA NGA GAL F:1;
G:1;
 Valid;
Valid;
 none;
none;
 submit data
819.74 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: GAL SIA NGA GAL; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA NGA GAL 1 1
2 SIA GAL NGA GAL 0.792453 0.981132
3 BGC GAL SIA NGA GAL 0.724138 0.981132
4 GAL SIA NGA GAL SIA 0.696429 0.981132
5 GAL NGA GAL SIA 0.681416 0.981132
6 BGC GAL SIA NGA GAL SIA 0.658333 0.981132
7 A2G GAL SIA 0.645455 0.981132
8 BGC GAL GLA NGA GAL SIA 0.639344 0.981132
9 GAL SIA NGA GAL SIA SIA 0.624 0.962963
10 GAL NAG GAL SIA 0.623932 1
11 GAL SIA NGA 0.619469 0.981132
12 BGC GAL SIA NGA GAL FUC 0.610687 0.981132
13 GAL NGA GAL SIA SIA 0.606299 0.962963
14 NAG GAL SIA 0.596491 0.981132
15 NAG GAL SIA SIA 0.591667 1
16 NDG GAL SIA SIA 0.591667 0.963636
17 BGC GAL SIA NAG 0.585366 0.981132
18 NGA GAL SIA 0.584746 0.962264
19 NAG 2FG SIA 0.581197 0.912281
20 NAG FUC GAL SIA 0.577236 0.981132
21 MAG FUC GAL SIA 0.577236 0.944444
22 GAL NAG FUC GAL SIA 0.574803 0.981132
23 2FG SIA 0.564815 0.877193
24 NGS GAL SIA 0.560976 0.776119
25 NGA POL GAL NGC AZI 0.550388 0.772727
26 NAG GAL NGC 0.54918 0.944444
27 NGS FUC GLA SIA 0.545455 0.776119
28 BGC GAL SIA SIA 0.543307 0.962963
29 BGC CEQ GAL SLB NGA GAL SIA SIA 0.537931 0.825397
30 BGC GAL SIA 0.537815 0.962264
31 BGC 18C GAL SIA NGA GAL 0.535484 0.854839
32 Z3Q GAL 5N6 0.534884 0.825397
33 BGC GAL SIA NGA SIA 0.525547 0.962963
34 GLC GAL NGC 0.520661 0.907407
35 MBG NGC 0.513274 0.890909
36 GAL SIA SIA 0.512605 0.962963
37 NAG GAL NAG GAL SIA 0.511278 1
38 GAL SIA 0.509259 0.943396
39 BGC GAL NAG GAL SIA 0.507463 1
40 GAL 5N6 0.504348 0.944444
41 NAG GAL PKM 0.480315 0.962963
42 NAG GAL 5N6 0.469231 0.981481
43 SIA CMO 0.465347 0.854545
44 BGC 16C GAL SIA 0.46 0.854839
45 NAG SIA 0.456897 0.928571
46 BGC 18C GAL SIA 0.453947 0.854839
47 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.428571 0.963636
48 MNA 0.427184 0.836364
49 C4W NAG FUC BMA MAN NAG GAL SIA 0.424051 0.868852
50 A2G SER GAL 0.423423 0.890909
51 CEQ BGC NGA GAL SIA SIA 0.423077 0.815385
52 MGC GAL 0.421569 0.851852
53 GLA NAG FUC GAL 0.420168 0.886792
54 WIA SIA 0.420168 0.912281
55 BGC GAL NGA GAL 0.419643 0.849057
56 A2G THR GAL 0.419643 0.925926
57 BGC GAL NAG GAL 0.412281 0.849057
58 GAL NAG GAL FUC 0.411765 0.90566
59 SIA SIA 0.410256 0.944444
60 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.408284 0.868852
61 SLB SIA SIA 0.40678 0.944444
62 SLB SIA SIA SIA 0.40678 0.944444
63 SLB SIA SIA SIA SIA 0.40678 0.944444
64 SIA SIA SIA SIA SIA SIA SIA 0.40678 0.944444
65 A2G NPO GAL 0.405172 0.731343
66 SIA SIA SIA 0.401639 0.944444
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL SIA NGA GAL; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: GAL SIA 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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