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+]
SIA GAL BGC NGA GAL C:301;
D:301;
Valid;
Valid;
none;
none;
submit data
997.88 n/a O=C([...
GAL SIA NGA GAL B:302;
Valid;
none;
submit data
835.739 n/a O=C([...
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 (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 42 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 4POR - BGC SIA GAL n/a n/a
11 4POS - NAG SIA GAL n/a n/a
12 4POT - NAG GAL NGC n/a n/a
13 4MJ0 - BGC SIA SIA GAL n/a n/a
14 3NXD - BGC GAL NAG SIA GAL n/a n/a
15 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
16 4X15 - SIA GAL BGC NGA n/a n/a
17 4X10 - SIA GAL BGC NGA n/a n/a
18 4X0Z - SIA GAL BGC NGA GAL n/a n/a
19 4JCF - SIA GAL NAG n/a n/a
20 4X12 - SIA SIA n/a n/a
21 4X14 - SIA GAL BGC NGA GAL n/a n/a
22 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
23 4X13 - SIA GAL NAG GAL BGC n/a n/a
24 4MBY - SIA GAL n/a n/a
25 4MBZ - SIA GAL n/a n/a
26 4FMI - NAG SIA GAL n/a n/a
27 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
28 4FMH - SIA GAL 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 GAL BGC NGA GAL; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA NGA GAL 1 1
2 SIA GAL BGC NGA GAL 1 1
3 GAL NGA SIA GAL BGC 1 1
4 GAL NGA GAL BGC SIA 1 1
5 BGC GAL SIA SIA GAL NGA 0.917431 1
6 GAL BGC GAL SIA NGA SIA 0.917431 1
7 GAL SIA NGA GAL 0.834862 1
8 GAL BGC SIA NGA 0.830357 1
9 BGC GAL SIA NGA 0.830357 1
10 SIA GAL BGC NGA 0.830357 1
11 SIA GAL NGA GAL 0.818182 1
12 GAL NGA GAL SIA 0.818182 1
13 GAL SIA NGA GAL SIA 0.769912 1
14 GAL BGC SIA 0.761468 0.961538
15 SIA GAL GLC 0.761468 0.961538
16 BGC SIA GAL 0.761468 0.961538
17 SIA BGC GAL 0.761468 0.961538
18 BGC GAL SIA 0.761468 0.961538
19 GLA GLC SIA 0.761468 0.961538
20 SIA GAL BGC 0.761468 0.961538
21 SIA GAL SIA BGC NGA 0.738095 0.981132
22 SIA GAL SIA GLC NGA 0.738095 0.981132
23 SIA SIA GAL NGA GAL 0.725806 0.981132
24 BGC GAL SIA NGA GAL SIA 0.704545 0.852459
25 SIA SIA GAL NGA GAL SIA 0.690476 0.981132
26 SIA SIA GLA BGC 0.674797 0.981132
27 BGC SIA SIA GAL 0.674797 0.981132
28 BGC GAL CEQ SLB NGA GAL SIA SIA 0.664286 0.866667
29 SIA GAL NGA 0.663793 1
30 MN0 GAL GLC 0.65812 0.924528
31 SLT 0.652174 0.942308
32 BGC 18C GAL NGA SIA GAL 0.642384 0.83871
33 SIA GAL NAG 0.641026 1
34 NAG SIA GAL 0.641026 1
35 NGA GAL SIA 0.632479 1
36 SIA GAL A2G 0.632479 1
37 BGC GAL NAG SIA GAL 0.630769 0.981132
38 SIA GAL NAG GAL GLC 0.630769 0.981132
39 SIA GAL NAG GAL BGC 0.630769 0.981132
40 SIA NAG GAL GAL 0.6 0.981132
41 4U0 0.595041 0.924528
42 NAG GAL NGC 0.592 0.962264
43 SIA GAL NGS 0.590551 0.8125
44 SIA GAL NAG SIA 0.582677 0.981132
45 SIA GAL NAG FUC 0.581395 1
46 SIA GLA NAG FUC 0.581395 1
47 NAG FUC SIA GAL 0.581395 1
48 SIA GAL NDG FUC 0.581395 1
49 SIA GAL MAG FUC 0.581395 0.962264
50 NDG FUC SIA GAL 0.581395 1
51 FUC NDG GAL SIA 0.581395 1
52 SIA GAL NDG SIA 0.55814 0.945455
53 SIA GAL 0.557522 0.961538
54 BGC GAL NAG GAL 0.554545 0.865385
55 GAL NAG GAL BGC 0.554545 0.865385
56 LAT NAG GAL 0.554545 0.865385
57 NAG GAL SIA 0.552 0.981132
58 GAL TNR SIA 0.550388 0.962963
59 GAL NGA GLA BGC GAL 0.548673 0.865385
60 SIA NAG GAL 0.547619 0.945455
61 SIA 2FG NAG 0.547619 0.928571
62 4U2 0.544715 0.980769
63 SIA GLA NGS FUC 0.539568 0.8125
64 GAL NAG SIA GAL 0.533835 0.981132
65 SIA GAL NAG GAL 0.533835 0.981132
66 NGC GAL NGA POL AZI 0.532847 0.784615
67 SIA 2FG 0.529915 0.892857
68 SIA GAL SIA BGC NGA CEQ 0.526316 0.8
69 Z3Q GAL 5N6 0.518248 0.83871
70 SIA GAL BGC 16C 0.506579 0.83871
71 4U1 0.503876 0.962264
72 5N6 GAL 0.5 0.962264
73 SIA SIA GAL 0.496063 0.981132
74 BGC 18C GAL SIA 0.490323 0.83871
75 NGC MBG 0.483607 0.907407
76 GAL SIA 0.483051 0.943396
77 FUC GAL NAG GAL BGC 0.472 0.884615
78 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.466667 0.962963
79 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.466667 0.962963
80 GLC GAL NAG GAL 0.466102 0.865385
81 GLA GAL NAG FUC GAL GLC 0.465116 0.884615
82 NGA GLA GAL BGC 0.45 0.865385
83 GLC GAL NAG GAL FUC FUC 0.446154 0.903846
84 BGC GAL NAG GAL FUC FUC 0.446154 0.903846
85 NAG GAL BGC 0.444444 0.865385
86 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.435065 0.962963
87 A2G GAL NAG FUC GAL GLC 0.426471 0.942308
88 GLC GAL NAG GAL FUC A2G 0.426471 0.942308
89 SIA CMO 0.423423 0.87037
90 NGA GAL BGC 0.422414 0.865385
91 GLA GAL BGC 0.4 0.634615
92 GLA GAL GAL 0.4 0.634615
Ligand no: 2; Ligand: GAL SIA NGA GAL; Similar ligands found: 102
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA NGA GAL 1 1
2 GAL SIA NGA GAL SIA 0.881188 1
3 SIA GAL BGC NGA GAL 0.834862 1
4 BGC GAL SIA NGA GAL 0.834862 1
5 GAL NGA SIA GAL BGC 0.834862 1
6 GAL NGA GAL BGC SIA 0.834862 1
7 SIA GAL NGA 0.794118 1
8 SIA SIA GAL NGA GAL SIA 0.780702 0.981132
9 BGC GAL SIA SIA GAL NGA 0.761062 1
10 GAL BGC GAL SIA NGA SIA 0.761062 1
11 GAL NGA GAL SIA 0.743119 1
12 SIA GAL NGA GAL 0.743119 1
13 SIA GAL BGC NGA 0.681035 1
14 BGC GAL SIA NGA 0.681035 1
15 GAL BGC SIA NGA 0.681035 1
16 SIA SIA GAL NGA GAL 0.672131 0.981132
17 BGC GAL SIA 0.669725 0.961538
18 GAL BGC SIA 0.669725 0.961538
19 SIA BGC GAL 0.669725 0.961538
20 SIA GAL GLC 0.669725 0.961538
21 BGC SIA GAL 0.669725 0.961538
22 SIA GAL BGC 0.669725 0.961538
23 GLA GLC SIA 0.669725 0.961538
24 SIA NAG GAL GAL 0.666667 0.981132
25 SIA GAL A2G 0.66055 1
26 NGA GAL SIA 0.66055 1
27 SIA GAL 0.627451 0.961538
28 NAG SIA GAL 0.625 1
29 SIA GAL NAG 0.625 1
30 SIA GAL SIA GLC NGA 0.620155 0.981132
31 SIA GAL SIA BGC NGA 0.620155 0.981132
32 NAG FUC SIA GAL 0.616667 1
33 FUC NDG GAL SIA 0.616667 1
34 SIA GLA NAG FUC 0.616667 1
35 SIA GAL NAG FUC 0.616667 1
36 SIA GAL NDG FUC 0.616667 1
37 NDG FUC SIA GAL 0.616667 1
38 BGC GAL SIA NGA GAL SIA 0.616541 0.852459
39 BGC GAL CEQ SLB NGA GAL SIA SIA 0.615942 0.866667
40 SIA SIA GLA BGC 0.606557 0.981132
41 BGC SIA SIA GAL 0.606557 0.981132
42 SIA GAL NAG SIA 0.605042 0.981132
43 GAL TNR SIA 0.596639 0.962963
44 SIA 2FG NAG 0.594828 0.928571
45 SIA GAL MAG FUC 0.590164 0.962264
46 BGC 18C GAL NGA SIA GAL 0.586667 0.83871
47 SIA NAG GAL 0.581197 0.945455
48 SIA 2FG 0.579439 0.892857
49 NAG GAL NGC 0.575 0.962264
50 MN0 GAL GLC 0.57265 0.924528
51 SIA GAL NDG SIA 0.565574 0.945455
52 SLT 0.565217 0.942308
53 SIA SIA GAL 0.565217 0.981132
54 SIA GAL NAG GAL 0.564516 0.981132
55 GAL NAG SIA GAL 0.564516 0.981132
56 SIA GAL NGS 0.560976 0.8125
57 NAG GAL SIA 0.559322 0.981132
58 SIA GAL NAG GAL GLC 0.553846 0.981132
59 SIA GAL NAG GAL BGC 0.553846 0.981132
60 BGC GAL NAG SIA GAL 0.553846 0.981132
61 NGC GAL NGA POL AZI 0.550388 0.784615
62 SIA GLA NGS FUC 0.545455 0.8125
63 5N6 GAL 0.544643 0.962264
64 4U0 0.537815 0.924528
65 4U2 0.525424 0.980769
66 Z3Q GAL 5N6 0.523077 0.83871
67 GAL SIA 0.513761 0.943396
68 NGC MBG 0.513274 0.907407
69 4U1 0.508197 0.962264
70 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.5 0.962963
71 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.5 0.962963
72 SIA GAL SIA BGC NGA CEQ 0.48 0.8
73 SIA GAL BGC 16C 0.47973 0.83871
74 BGC 18C GAL SIA 0.473333 0.83871
75 SIA CMO 0.465347 0.87037
76 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.465278 0.962963
77 LAT NAG GAL 0.463636 0.865385
78 GAL NAG GAL BGC 0.463636 0.865385
79 BGC GAL NAG GAL 0.463636 0.865385
80 GAL NGA GLA BGC GAL 0.460177 0.865385
81 SIA NAG 0.432203 0.910714
82 SIA WIA 0.432203 0.894737
83 A2G SER GAL 0.431193 0.90566
84 NGA SER GAL 0.431193 0.90566
85 GAL TNR 0.431193 0.90566
86 GAL SER A2G 0.431193 0.90566
87 MNA 0.427184 0.851852
88 SIA SIA 0.422414 0.962264
89 SLB SIA 0.422414 0.962264
90 GAL MGC 0.421569 0.867925
91 GAL A2G THR 0.419643 0.961538
92 SLB SIA SIA SIA SIA 0.418803 0.962264
93 SLB SIA SIA 0.418803 0.962264
94 SIA SIA SIA SLB 0.418803 0.962264
95 SIA SIA SIA SIA SIA SIA SIA 0.418803 0.962264
96 SIA SIA SIA 0.413223 0.962264
97 GLA NAG GAL FUC 0.410256 0.884615
98 GAL NAG GAL FUC 0.410256 0.884615
99 GAL NGA 0.407767 0.865385
100 GAL A2G 0.407767 0.865385
101 A2G GAL 0.407767 0.865385
102 FUC BGC GAL NAG GAL 0.4 0.884615
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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