Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL C:304;
E:303;
A:301;
D:304;
A:305;
D:303;
E:305;
B:305;
A:302;
C:307;
E:304;
A:304;
D:306;
C:308;
C:306;
E:301;
B:304;
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;
submit data
92.094 C3 H8 O3 C(C(C...
EDO B:302;
E:302;
C:303;
C:305;
A:303;
D:305;
B:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
K A:306;
D:307;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
SIA SIA D:301;
C:301;
Valid;
Valid;
none;
none;
submit data
598.511 n/a O=C([...
SIA B:301;
Valid;
none;
submit data
309.27 C11 H19 N O9 CC(=O...
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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
2 4X17 - SIA SIA 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: SIA SIA; Similar ligands found: 70
No: Ligand ECFP6 Tc MDL keys Tc
1 SLB SIA 1 1
2 SIA SIA 1 1
3 SIA SIA SIA SIA SIA SIA SIA 0.985915 1
4 SLB SIA SIA 0.985915 1
5 SLB SIA SIA SIA SIA 0.985915 1
6 SIA SIA SIA SLB 0.985915 1
7 SIA SIA SIA 0.717647 1
8 SIA SIA GAL 0.648936 0.981132
9 SIA CMO 0.64 0.87037
10 SLB 0.565789 0.826923
11 SIA 0.565789 0.826923
12 SIA SIA GLA BGC 0.554545 0.981132
13 BGC SIA SIA GAL 0.554545 0.981132
14 MNA 0.544304 0.851852
15 GAL SIA 0.521739 0.907407
16 SIA SIA GAL NGA GAL SIA 0.521368 0.981132
17 SIA SIA GAL NGA GAL 0.516949 0.981132
18 SIA GAL 0.516129 0.924528
19 SIA 2FG 0.5 0.859649
20 SIA GAL SIA BGC NGA 0.495935 0.981132
21 SIA GAL SIA GLC NGA 0.495935 0.981132
22 SIA NAG 0.484536 0.910714
23 18D 0.464286 0.796296
24 42D 0.464286 0.8
25 CNP 0.45977 0.767857
26 MUS 0.456311 0.79661
27 SIA GAL NGA 0.449541 0.962264
28 SIA GAL SIA BGC NGA CEQ 0.448529 0.8
29 BGC GAL CEQ SLB NGA GAL SIA SIA 0.445255 0.866667
30 NGA GAL SIA 0.444444 0.962264
31 SIA GAL A2G 0.444444 0.962264
32 NGC 0.440476 0.811321
33 SIA BGC GAL 0.440367 0.924528
34 BGC GAL SIA 0.440367 0.924528
35 SIA GAL BGC 0.440367 0.924528
36 NAG SIA GAL 0.440367 0.962264
37 SIA GAL NAG 0.440367 0.962264
38 SIA GAL GLC 0.440367 0.924528
39 GLA GLC SIA 0.440367 0.924528
40 BGC SIA GAL 0.440367 0.924528
41 GAL BGC SIA 0.440367 0.924528
42 MN0 0.436782 0.818182
43 NAG GAL SIA 0.432432 0.944444
44 SIA NAG GAL 0.428571 0.910714
45 SIA 2FG NAG 0.428571 0.894737
46 5N6 GAL 0.423077 0.925926
47 GAL SIA NGA GAL SIA 0.422414 0.962264
48 GAL SIA NGA GAL 0.422414 0.962264
49 GAL TNR SIA 0.422414 0.927273
50 NDG FUC SIA GAL 0.420168 0.962264
51 FUC NDG GAL SIA 0.420168 0.962264
52 SIA GAL MAG FUC 0.420168 0.962264
53 SIA GLA NAG FUC 0.420168 0.962264
54 NAG FUC SIA GAL 0.420168 0.962264
55 SIA GAL NAG FUC 0.420168 0.962264
56 SIA GAL NDG FUC 0.420168 0.962264
57 SID 0.417582 0.785714
58 NGC MBG 0.417476 0.907407
59 SIA WIA 0.411765 0.862069
60 GAL NGA GAL SIA 0.410256 0.962264
61 SIA GAL NGA GAL 0.410256 0.962264
62 SIA NAG GAL GAL 0.410256 0.944444
63 NXD 0.408602 0.793103
64 SIA GAL NDG SIA 0.40678 0.910714
65 SIA GAL NAG SIA 0.40678 0.944444
66 C5P SIA 0.406504 0.666667
67 425 0.405405 0.662338
68 SIA GAL NGS 0.403361 0.784615
69 NAG GAL NGC 0.401709 0.925926
70 79J 0.4 0.849057
Ligand no: 2; Ligand: SIA; Similar ligands found: 49
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 18D 0.758621 0.955556
4 42D 0.758621 0.875
5 NGC 0.754386 0.933333
6 MNA 0.629032 0.895833
7 79J 0.615385 0.934783
8 SIA CMO 0.59375 0.877551
9 CNP 0.58209 0.875
10 KDN 0.568965 0.72093
11 KDM 0.568965 0.72093
12 SIA SIA 0.565789 0.826923
13 SLB SIA 0.565789 0.826923
14 SIA SIA SIA SLB 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 SLB SIA SIA SIA SIA 0.558442 0.826923
17 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
18 FSI 0.515152 0.895833
19 SFJ 0.5 0.875
20 6KL 0.5 0.807692
21 MN0 0.485714 0.895833
22 EQP 0.470588 0.788462
23 AXP 0.470588 0.788462
24 GAL SIA 0.469136 0.843137
25 SIA GAL 0.463415 0.86
26 SID 0.459459 0.82
27 SIA SIA SIA 0.453488 0.826923
28 MUS 0.449438 0.796296
29 NXD 0.447368 0.792453
30 SIA 2FG 0.447059 0.796296
31 SIA WIA 0.447059 0.767857
32 SLT 0.44086 0.877551
33 KDO 0.435484 0.704545
34 SIA NAG 0.430233 0.781818
35 4U0 0.427083 0.86
36 4U2 0.425532 0.843137
37 BND 0.416667 0.807692
38 SKD 0.414286 0.875
39 SIA SIA GAL 0.410526 0.811321
40 4U1 0.408163 0.826923
41 GLA GLC SIA 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 SIA BGC GAL 0.402062 0.86
44 BGC GAL SIA 0.402062 0.86
45 SIA GAL GLC 0.402062 0.86
46 BGC SIA GAL 0.402062 0.86
47 SIA GAL BGC 0.402062 0.86
48 4AM 0.4 0.833333
49 DAN 0.4 0.911111
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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