Receptor
PDB id Resolution Class Description Source Keywords
4X15 2.11 Å NON-ENZYME: OTHER JC MAD-1 POLYOMAVIRUS VP1 IN COMPLEX WITH GM2 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
GOL D:308;
D:305;
A:301;
B:305;
C:305;
E:301;
A:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
EDO B:306;
D:307;
E:302;
C:306;
B:307;
E:303;
D:306;
C:307;
C:308;
A:304;
A:302;
A:305;
E:304;
C:309;
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;
submit data
62.068 C2 H6 O2 C(CO)...
SIA GAL BGC NGA C:301;
D:301;
Valid;
Valid;
none;
none;
submit data
835.739 n/a O=C([...
GAL BGC SIA NGA B:302;
Valid;
none;
submit data
835.739 n/a O=C([...
K A:306;
D:309;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
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; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL BGC SIA NGA 1 1
2 BGC GAL SIA NGA 1 1
3 SIA GAL BGC NGA 1 1
4 SIA GAL SIA BGC NGA 0.877193 0.981132
5 SIA GAL SIA GLC NGA 0.877193 0.981132
6 BGC GAL SIA NGA GAL 0.830357 1
7 SIA GAL BGC NGA GAL 0.830357 1
8 GAL NGA SIA GAL BGC 0.830357 1
9 GAL NGA GAL BGC SIA 0.830357 1
10 SIA GAL NGA 0.807692 1
11 BGC GAL SIA SIA GAL NGA 0.80531 1
12 GAL BGC GAL SIA NGA SIA 0.80531 1
13 GLA GLC SIA 0.747664 0.961538
14 BGC SIA GAL 0.747664 0.961538
15 SIA BGC GAL 0.747664 0.961538
16 SIA GAL BGC 0.747664 0.961538
17 SIA GAL GLC 0.747664 0.961538
18 BGC GAL SIA 0.747664 0.961538
19 GAL BGC SIA 0.747664 0.961538
20 GAL NGA GAL SIA 0.710526 1
21 SIA GAL NGA GAL 0.710526 1
22 GAL SIA NGA GAL 0.681035 1
23 MN0 GAL GLC 0.672566 0.924528
24 GAL SIA NGA GAL SIA 0.666667 1
25 SIA SIA GLA BGC 0.661157 0.981132
26 BGC SIA SIA GAL 0.661157 0.981132
27 SLT 0.637168 0.942308
28 SIA SIA GAL NGA GAL 0.632812 0.981132
29 SIA GAL NAG 0.626087 1
30 NAG SIA GAL 0.626087 1
31 BGC GAL SIA NGA GAL SIA 0.617647 0.852459
32 BGC GAL NAG SIA GAL 0.617188 0.981132
33 SIA GAL NAG GAL GLC 0.617188 0.981132
34 SIA GAL NAG GAL BGC 0.617188 0.981132
35 NAG GAL NGC 0.603306 0.962264
36 SIA SIA GAL NGA GAL SIA 0.6 0.981132
37 4U0 0.579832 0.924528
38 SIA GAL A2G 0.576271 1
39 NGA GAL SIA 0.576271 1
40 SIA GAL NGS 0.576 0.8125
41 BGC GAL CEQ SLB NGA GAL SIA SIA 0.572414 0.866667
42 SIA GAL 0.568807 0.961538
43 SIA GAL SIA BGC NGA CEQ 0.544218 0.8
44 GAL NAG SIA GAL 0.542636 0.981132
45 NDG FUC SIA GAL 0.542636 1
46 SIA GAL NAG FUC 0.542636 1
47 FUC NDG GAL SIA 0.542636 1
48 NAG FUC SIA GAL 0.542636 1
49 SIA GAL NDG FUC 0.542636 1
50 SIA GAL NAG GAL 0.542636 0.981132
51 SIA GLA NAG FUC 0.542636 1
52 SIA 2FG 0.539823 0.892857
53 BGC 18C GAL NGA SIA GAL 0.537975 0.83871
54 NAG GAL SIA 0.536585 0.981132
55 SIA 2FG NAG 0.532258 0.928571
56 SIA GAL NAG SIA 0.53125 0.981132
57 SIA GAL NDG SIA 0.53125 0.945455
58 SIA GAL MAG FUC 0.530769 0.962264
59 4U2 0.528926 0.980769
60 NGA GAL BGC 0.52381 0.865385
61 NAG GAL BGC 0.518519 0.865385
62 NGA GLA GAL BGC 0.508929 0.865385
63 NGC MBG 0.504274 0.907407
64 SIA SIA GAL 0.504065 0.981132
65 SIA GLA NGS FUC 0.503597 0.8125
66 SIA NAG GAL GAL 0.5 0.981132
67 SIA NAG GAL 0.496063 0.945455
68 5N6 GAL 0.495798 0.962264
69 GAL SIA 0.491228 0.943396
70 4U1 0.488189 0.962264
71 NGC GAL NGA POL AZI 0.485507 0.784615
72 SIA GAL BGC 16C 0.483444 0.83871
73 BGC 18C GAL SIA 0.467532 0.83871
74 GAL TNR SIA 0.466165 0.962963
75 Z3Q GAL 5N6 0.45 0.83871
76 GLC GAL NAG GAL 0.448276 0.865385
77 SIA CMO 0.443396 0.87037
78 NAG MUB 0.431034 0.961538
79 NAG AMU 0.431034 0.961538
80 A2G GAL BGC FUC 0.430894 0.884615
81 A2G GAL NAG FUC GAL GLC 0.421053 0.942308
82 GLC GAL NAG GAL FUC A2G 0.421053 0.942308
83 BGC GAL NAG GAL 0.418803 0.865385
84 GAL NAG GAL BGC 0.418803 0.865385
85 LAT NAG GAL 0.418803 0.865385
86 GAL NGA GLA BGC GAL 0.416667 0.865385
87 NAG AMU NAG AMV 0.414634 0.943396
88 NAG GAL NAG 0.413793 0.923077
89 CBS CBS 0.40367 0.923077
90 CBS 0.40367 0.923077
91 NAG NDG 0.40367 0.923077
92 NAG GDL 0.40367 0.923077
93 NDG NAG NAG 0.401786 0.942308
94 NDG NAG NAG NAG 0.401786 0.942308
95 CTO 0.401786 0.942308
96 NAG NAG NAG NAG NDG 0.401786 0.942308
97 NAG NAG NAG NAG NAG NAG NAG NAG 0.401786 0.942308
98 NAG NAG NAG NAG 0.401786 0.942308
99 NAG NAG NAG 0.401786 0.942308
100 NAG NAG NDG 0.401786 0.942308
101 NAG NAG NAG NAG NDG NAG 0.401786 0.942308
102 NAG NAG NAG NAG NAG NAG 0.401786 0.942308
103 NAG NAG NAG NDG 0.401786 0.942308
104 NDG NAG NAG NDG NAG 0.401786 0.942308
105 NAG NAG NAG NAG NAG 0.401786 0.942308
106 NDG NAG NAG NDG 0.401786 0.942308
Ligand no: 2; Ligand: GAL BGC SIA NGA; Similar ligands found: 106
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL BGC SIA NGA 1 1
2 BGC GAL SIA NGA 1 1
3 SIA GAL BGC NGA 1 1
4 SIA GAL SIA BGC NGA 0.877193 0.981132
5 SIA GAL SIA GLC NGA 0.877193 0.981132
6 BGC GAL SIA NGA GAL 0.830357 1
7 SIA GAL BGC NGA GAL 0.830357 1
8 GAL NGA SIA GAL BGC 0.830357 1
9 GAL NGA GAL BGC SIA 0.830357 1
10 SIA GAL NGA 0.807692 1
11 BGC GAL SIA SIA GAL NGA 0.80531 1
12 GAL BGC GAL SIA NGA SIA 0.80531 1
13 GLA GLC SIA 0.747664 0.961538
14 BGC SIA GAL 0.747664 0.961538
15 SIA BGC GAL 0.747664 0.961538
16 SIA GAL BGC 0.747664 0.961538
17 SIA GAL GLC 0.747664 0.961538
18 BGC GAL SIA 0.747664 0.961538
19 GAL BGC SIA 0.747664 0.961538
20 GAL NGA GAL SIA 0.710526 1
21 SIA GAL NGA GAL 0.710526 1
22 GAL SIA NGA GAL 0.681035 1
23 MN0 GAL GLC 0.672566 0.924528
24 GAL SIA NGA GAL SIA 0.666667 1
25 SIA SIA GLA BGC 0.661157 0.981132
26 BGC SIA SIA GAL 0.661157 0.981132
27 SLT 0.637168 0.942308
28 SIA SIA GAL NGA GAL 0.632812 0.981132
29 SIA GAL NAG 0.626087 1
30 NAG SIA GAL 0.626087 1
31 BGC GAL SIA NGA GAL SIA 0.617647 0.852459
32 BGC GAL NAG SIA GAL 0.617188 0.981132
33 SIA GAL NAG GAL GLC 0.617188 0.981132
34 SIA GAL NAG GAL BGC 0.617188 0.981132
35 NAG GAL NGC 0.603306 0.962264
36 SIA SIA GAL NGA GAL SIA 0.6 0.981132
37 4U0 0.579832 0.924528
38 SIA GAL A2G 0.576271 1
39 NGA GAL SIA 0.576271 1
40 SIA GAL NGS 0.576 0.8125
41 BGC GAL CEQ SLB NGA GAL SIA SIA 0.572414 0.866667
42 SIA GAL 0.568807 0.961538
43 SIA GAL SIA BGC NGA CEQ 0.544218 0.8
44 GAL NAG SIA GAL 0.542636 0.981132
45 NDG FUC SIA GAL 0.542636 1
46 SIA GAL NAG FUC 0.542636 1
47 FUC NDG GAL SIA 0.542636 1
48 NAG FUC SIA GAL 0.542636 1
49 SIA GAL NDG FUC 0.542636 1
50 SIA GAL NAG GAL 0.542636 0.981132
51 SIA GLA NAG FUC 0.542636 1
52 SIA 2FG 0.539823 0.892857
53 BGC 18C GAL NGA SIA GAL 0.537975 0.83871
54 NAG GAL SIA 0.536585 0.981132
55 SIA 2FG NAG 0.532258 0.928571
56 SIA GAL NAG SIA 0.53125 0.981132
57 SIA GAL NDG SIA 0.53125 0.945455
58 SIA GAL MAG FUC 0.530769 0.962264
59 4U2 0.528926 0.980769
60 NGA GAL BGC 0.52381 0.865385
61 NAG GAL BGC 0.518519 0.865385
62 NGA GLA GAL BGC 0.508929 0.865385
63 NGC MBG 0.504274 0.907407
64 SIA SIA GAL 0.504065 0.981132
65 SIA GLA NGS FUC 0.503597 0.8125
66 SIA NAG GAL GAL 0.5 0.981132
67 SIA NAG GAL 0.496063 0.945455
68 5N6 GAL 0.495798 0.962264
69 GAL SIA 0.491228 0.943396
70 4U1 0.488189 0.962264
71 NGC GAL NGA POL AZI 0.485507 0.784615
72 SIA GAL BGC 16C 0.483444 0.83871
73 BGC 18C GAL SIA 0.467532 0.83871
74 GAL TNR SIA 0.466165 0.962963
75 Z3Q GAL 5N6 0.45 0.83871
76 GLC GAL NAG GAL 0.448276 0.865385
77 SIA CMO 0.443396 0.87037
78 NAG MUB 0.431034 0.961538
79 NAG AMU 0.431034 0.961538
80 A2G GAL BGC FUC 0.430894 0.884615
81 A2G GAL NAG FUC GAL GLC 0.421053 0.942308
82 GLC GAL NAG GAL FUC A2G 0.421053 0.942308
83 BGC GAL NAG GAL 0.418803 0.865385
84 GAL NAG GAL BGC 0.418803 0.865385
85 LAT NAG GAL 0.418803 0.865385
86 GAL NGA GLA BGC GAL 0.416667 0.865385
87 NAG AMU NAG AMV 0.414634 0.943396
88 NAG GAL NAG 0.413793 0.923077
89 CBS CBS 0.40367 0.923077
90 CBS 0.40367 0.923077
91 NAG NDG 0.40367 0.923077
92 NAG GDL 0.40367 0.923077
93 NDG NAG NAG 0.401786 0.942308
94 NDG NAG NAG NAG 0.401786 0.942308
95 CTO 0.401786 0.942308
96 NAG NAG NAG NAG NDG 0.401786 0.942308
97 NAG NAG NAG NAG NAG NAG NAG NAG 0.401786 0.942308
98 NAG NAG NAG NAG 0.401786 0.942308
99 NAG NAG NAG 0.401786 0.942308
100 NAG NAG NDG 0.401786 0.942308
101 NAG NAG NAG NAG NDG NAG 0.401786 0.942308
102 NAG NAG NAG NAG NAG NAG 0.401786 0.942308
103 NAG NAG NAG NDG 0.401786 0.942308
104 NDG NAG NAG NDG NAG 0.401786 0.942308
105 NAG NAG NAG NAG NAG 0.401786 0.942308
106 NDG NAG NAG NDG 0.401786 0.942308
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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