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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(N...
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 1443 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 (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 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 4X17 - SIA SIA n/a n/a
20 4JCF - SIA GAL NAG n/a n/a
21 4X12 - SIA SIA n/a n/a
22 4X14 - SIA GAL BGC NGA GAL n/a n/a
23 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
24 4X13 - SIA GAL NAG GAL BGC n/a n/a
25 4MBY - SIA GAL n/a n/a
26 4MBZ - SIA GAL n/a n/a
27 4FMI - NAG SIA GAL n/a n/a
28 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
29 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 35 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: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA 1 1
2 SLB SIA 1 1
3 SIA SIA SIA SIA SIA SIA SIA 0.985915 1
4 SLB SIA SIA 0.985915 1
5 SIA SIA SIA 0.717647 1
6 SIA SIA GAL 0.648936 0.981132
7 SIA 0.565789 0.826923
8 SLB 0.565789 0.826923
9 SIA SIA GLA BGC 0.554545 0.981132
10 BGC SIA SIA GAL 0.554545 0.981132
11 MNA 0.544304 0.851852
12 SIA SIA GAL NGA GAL SIA 0.521368 0.981132
13 SIA SIA GAL NGA GAL 0.516949 0.981132
14 GAL SIA 0.516129 0.924528
15 SIA 2FG 0.5 0.859649
16 SIA GAL SIA GLC NGA 0.495935 0.981132
17 SIA GAL SIA BGC NGA 0.495935 0.981132
18 SIA GAL 0.489583 0.888889
19 SIA NAG 0.484536 0.910714
20 42D 0.464286 0.8
21 18D 0.464286 0.796296
22 CNP 0.45977 0.767857
23 MUS 0.456311 0.79661
24 SIA GAL NGA 0.449541 0.962264
25 SIA GAL SIA BGC NGA CEQ 0.448529 0.8
26 BGC GAL CEQ SLB NGA GAL SIA SIA 0.445255 0.83871
27 SIA GAL A2G 0.444444 0.962264
28 NGA GAL SIA 0.444444 0.962264
29 NGC 0.440476 0.811321
30 NGE 0.440476 0.811321
31 GLA GLC SIA 0.440367 0.924528
32 SIA GAL BGC 0.440367 0.924528
33 NAG SIA GAL 0.440367 0.962264
34 BGC SIA GAL 0.440367 0.924528
35 SIA GAL GLC 0.440367 0.924528
36 GAL BGC SIA 0.440367 0.924528
37 BGC GAL SIA 0.440367 0.924528
38 MN0 0.436782 0.818182
39 NAG GAL SIA 0.432432 0.944444
40 SIA GAL NAG 0.428571 0.910714
41 SIA NAG GAL 0.428571 0.910714
42 SIA 2FG NAG 0.428571 0.894737
43 GAL SIA NGA GAL SIA 0.422414 0.962264
44 SIA GAL NGA GAL 0.422414 0.962264
45 GAL SIA NGA GAL 0.422414 0.962264
46 NDG FUC SIA GAL 0.420168 0.962264
47 NAG FUC SIA GAL 0.420168 0.962264
48 SIA GAL NDG FUC 0.420168 0.962264
49 SIA GLA NAG FUC 0.420168 0.962264
50 FUC NDG GAL SIA 0.420168 0.962264
51 SIA GAL NAG FUC 0.420168 0.962264
52 SIA GAL MAG FUC 0.420168 0.962264
53 GAL TNR SIA 0.418803 0.910714
54 SID 0.417582 0.785714
55 NGC MBG 0.417476 0.907407
56 SIA GAL NAG GAL 0.417391 0.944444
57 SIA GAL NGS 0.415254 0.761194
58 SIA WIA 0.411765 0.862069
59 SIA NAG GAL GAL 0.410256 0.944444
60 GAL NGA GAL SIA 0.410256 0.944444
61 NXD 0.408602 0.793103
62 SIA GAL NAG SIA 0.40678 0.944444
63 SIA GAL NDG SIA 0.40678 0.910714
64 C5P SIA 0.406504 0.666667
65 425 0.405405 0.662338
66 NAG GAL NGC 0.401709 0.925926
67 79J 0.4 0.849057
Ligand no: 2; Ligand: SIA; Similar ligands found: 47
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 NGE 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
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 SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 FSI 0.515152 0.895833
17 6KL 0.5 0.807692
18 SFJ 0.5 0.875
19 MN0 0.485714 0.895833
20 EQP 0.470588 0.788462
21 AXP 0.470588 0.788462
22 GAL SIA 0.463415 0.86
23 SID 0.459459 0.82
24 SIA SIA SIA 0.453488 0.826923
25 MUS 0.449438 0.796296
26 NXD 0.447368 0.792453
27 SIA WIA 0.447059 0.767857
28 SIA 2FG 0.447059 0.796296
29 SLT 0.44086 0.877551
30 KDO 0.435484 0.704545
31 SIA GAL 0.435294 0.86
32 SIA NAG 0.430233 0.781818
33 4U0 0.427083 0.86
34 4U2 0.425532 0.843137
35 BND 0.416667 0.807692
36 SKD 0.414286 0.875
37 SIA SIA GAL 0.410526 0.811321
38 4U1 0.408163 0.826923
39 E3M 0.402778 0.606061
40 SIA GAL GLC 0.402062 0.86
41 BGC SIA GAL 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 BGC GAL SIA 0.402062 0.86
44 SIA GAL BGC 0.402062 0.86
45 GLA GLC SIA 0.402062 0.86
46 4AM 0.4 0.833333
47 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 with APoc: 33
This union binding pocket(no: 1) in the query (biounit: 4x17.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1UW1 ADP None
2 5A89 ADP 1.28205
3 5A89 FMN 1.28205
4 1WRA PC 1.83824
5 5KJW 53C 2.20588
6 1JX6 AI2 2.20588
7 3PE2 E1B 2.57353
8 4S00 AKR 3.30882
9 5LIA 6XN 3.67647
10 1PZO CBT 3.80228
11 5WBF LAC 4.07407
12 4M1U A2G MBG 4.28571
13 2HRL SIA GAL SIA BGC NGA CEQ 4.72441
14 5KBF CMP 4.77941
15 1LR8 IHS 5.40541
16 2HJ9 AI2 5.42986
17 1NB9 ADP 5.44218
18 1NB9 RBF 5.44218
19 1M5B BN1 5.70342
20 2VWT PYR 5.99251
21 1Z0N BCD 6.25
22 1SU2 ATP 6.28931
23 4IPH 1FJ 6.50407
24 1U25 IHS 6.52819
25 4YEF 4CQ 6.74157
26 1XOC VAL ASP SER LYS ASN THR SER SER TRP 7.35294
27 3HAV SRY 7.35294
28 1GPM AMP 8.08823
29 3GE7 AFQ 8.82353
30 3UDG TMP 9.19118
31 2BOS GLA GAL GLC 11.7647
32 2BOS GLA GAL 11.7647
33 1KJ1 MAN 12.844
Pocket No.: 2; Query (leader) PDB : 4X17; Ligand: SIA SIA; Similar sites found with APoc: 34
This union binding pocket(no: 2) in the query (biounit: 4x17.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1UW1 ADP None
2 1SQL GUN None
3 5A89 FMN 1.28205
4 5A89 ADP 1.28205
5 1WRA PC 1.83824
6 5T9C G3P 1.86567
7 5KJW 53C 2.20588
8 1XSE NDP 2.57353
9 4S00 AKR 3.30882
10 3FSY SCA 3.31325
11 3NX2 FER 3.57143
12 4M1U A2G MBG 4.28571
13 4M1U MBG A2G 4.28571
14 3IOI 1GW 4.77941
15 3H55 GLA 4.77941
16 1LR8 IHS 5.40541
17 2HJ9 AI2 5.42986
18 1NB9 RBF 5.44218
19 1NB9 ADP 5.44218
20 2V5K OXM 5.51471
21 1M5B BN1 5.70342
22 2VWT PYR 5.99251
23 1Z0N BCD 6.25
24 4IPH 1FJ 6.50407
25 4EUO ABU 6.61765
26 4YEF 4CQ 6.74157
27 1XOC VAL ASP SER LYS ASN THR SER SER TRP 7.35294
28 5X2N ALA 8.82353
29 3GE7 AFQ 8.82353
30 1S4M LUM 9.19118
31 3UDG TMP 9.19118
32 2BOS GLA GAL GLC 11.7647
33 2BOS GLA GAL 11.7647
34 1BB6 UMG 14.7287
Pocket No.: 3; Query (leader) PDB : 4X17; Ligand: SIA SIA; Similar sites found with APoc: 36
This union binding pocket(no: 3) in the query (biounit: 4x17.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1C4Q GLA GAL BGC None
2 3I59 N6S 2.00803
3 3PE2 E1B 2.57353
4 1OFZ FUC 2.57353
5 1KPG SAH 2.57353
6 1KPH SAH 2.57353
7 3BJK CIT 2.61438
8 5MKG C2E 2.75591
9 3WDX BGC BGC GLC 3.30882
10 4FWE FAD 3.30882
11 3JZ0 CLY 3.30882
12 1NF3 GNP 3.58974
13 5LIA 6XN 3.67647
14 6AM8 PLT 3.67647
15 1QD1 FON 3.67647
16 1PZO CBT 3.80228
17 3OCP CMP 4.31655
18 1CX4 CMP 4.41176
19 3UN3 G16 4.41176
20 2ART LPA AMP 4.58015
21 2HRL SIA GAL SIA BGC NGA CEQ 4.72441
22 4ZDC CO8 4.77941
23 5KBF CMP 4.77941
24 5Z21 NAI 5.02793
25 1GT4 UNA 5.03145
26 6GR0 F8W 5.74713
27 1N07 FMN 6.13497
28 2GU8 796 6.61765
29 1VYF OLA 6.66667
30 3ZW2 GLA NAG GAL FUC 6.89655
31 3ZW2 NAG GAL FUC 6.89655
32 1U7Z PMT 7.9646
33 1GPM AMP 8.08823
34 4WNB 4BN 10.0775
35 1ZB6 GST 10.2941
36 1KJ1 MAN 12.844
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