Receptor
PDB id Resolution Class Description Source Keywords
4U61 1.65 Å NON-ENZYME: STRUCTURAL TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS (TSPYV) VP COMPLEX WITH 6'-SIALYLLACTOSE TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS VIRAL COAT PROTEIN JELLY-ROLL FOLD GLYCAN BINDING VIRAL P
Ref.: TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS U DISPLACED BINDING SITE ON VP1 TO ENGAGE SIALYLATED GLYCOLIPIDS. PLOS PATHOG. V. 11 05112 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL H:401;
E:402;
E:403;
C:401;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
GAL SIA K:1;
 Valid;
 none;
 submit data
454.405 n/a O=C(N...
SIA C:402;
J:401;
H:402;
I:401;
B:401;
E:401;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
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
4U60 1.5 Å NON-ENZYME: STRUCTURAL TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS (TSPYV) VP COMPLEX WITH GM1 OLIGOSACCHARIDE TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS VIRAL COAT PROTEIN JELLY-ROLL FOLD CARBOHYDRATE BINDING VPROTEIN
Ref.: TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS U DISPLACED BINDING SITE ON VP1 TO ENGAGE SIALYLATED GLYCOLIPIDS. PLOS PATHOG. V. 11 05112 2015
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4U60 - BGC GAL SIA NGA GAL n/a n/a
2 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
3 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
4 4U61 - GAL SIA n/a n/a
5 6HKU - GLC 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: GAL SIA; Similar ligands found: 60
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA 1 1
2 NAG SIA 0.710843 0.909091
3 SIA CMO 0.635135 0.867925
4 BGC GAL SIA 0.608247 0.980392
5 NDG GAL SIA SIA 0.592233 0.909091
6 GAL NAG GAL SIA 0.567308 0.943396
7 NAG GAL SIA SIA 0.561905 0.943396
8 MNA 0.558442 0.849057
9 2FG SIA 0.543478 0.890909
10 SIA SIA 0.516484 0.888889
11 NAG GAL NAG GAL SIA 0.513043 0.943396
12 SLB SIA SIA SIA 0.51087 0.888889
13 SLB SIA SIA SIA SIA 0.51087 0.888889
14 SLB SIA SIA 0.51087 0.888889
15 SIA SIA SIA SIA SIA SIA SIA 0.51087 0.888889
16 GAL SIA NGA GAL 0.509259 0.943396
17 BGC GAL NAG GAL SIA 0.508621 0.943396
18 NAG GAL 5N6 0.504587 0.925926
19 GAL SIA SIA 0.5 0.907407
20 A2G GAL SIA 0.495146 0.924528
21 NAG GAL SIA 0.490385 0.924528
22 GAL SIA NGA 0.485714 0.924528
23 SIA SIA SIA 0.484536 0.888889
24 GAL 5N6 0.474747 0.924528
25 NGS GAL SIA 0.473214 0.731343
26 SIA GAL NGA GAL 0.468468 0.924528
27 GAL NGA GAL SIA 0.468468 0.924528
28 GAL SIA NGA GAL SIA 0.468468 0.924528
29 NAG FUC GAL SIA 0.464912 0.924528
30 NAG 2FG SIA 0.462963 0.859649
31 SIA 0.4625 0.86
32 SLB 0.4625 0.86
33 MBG NGC 0.454545 0.90566
34 NGA GAL SIA 0.454545 0.90566
35 CNP 0.453488 0.796296
36 MAG FUC GAL SIA 0.452174 0.888889
37 NGS FUC GLA SIA 0.45082 0.731343
38 WIA SIA 0.44898 0.892857
39 MN0 0.447059 0.849057
40 NAG GAL NGC 0.446429 0.924528
41 GAL NAG FUC GAL SIA 0.441667 0.924528
42 BGC GAL SIA NAG 0.435897 0.924528
43 BGC GAL SIA NGA GAL SIA 0.433333 0.924528
44 BGC GAL SIA SIA 0.432203 0.907407
45 BGC GAL GLA NGA GAL SIA 0.429752 0.924528
46 BGC GAL SIA NGA GAL 0.429752 0.924528
47 SID 0.426966 0.781818
48 C5P SIA 0.425 0.662162
49 MUS 0.423077 0.793103
50 GAL SIA NGA GAL SIA SIA 0.419355 0.907407
51 NXD 0.417582 0.789474
52 GAL NGA GAL SIA SIA 0.416 0.907407
53 C4W NAG FUC BMA MAN NAG GAL SIA 0.414286 0.819672
54 423 0.407407 0.636364
55 6KL 0.406977 0.77193
56 GLY PRO ALA THR PRO ALA PRO A2G SIA 0.406897 0.724638
57 NGA POL GAL NGC AZI 0.406504 0.753846
58 GLC GAL NGC 0.401786 0.923077
59 PH5 0.4 0.888889
60 425 0.4 0.636364
Ligand no: 2; Ligand: SIA; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 42D 0.758621 0.875
4 18D 0.758621 0.955556
5 NGE 0.754386 0.933333
6 NGC 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
9 SIA CMO 0.59375 0.877551
10 CNP 0.58209 0.875
11 KDM 0.568965 0.72093
12 KDN 0.568965 0.72093
13 SIA SIA 0.565789 0.826923
14 SLB SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA SIA 0.558442 0.826923
16 SLB 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 0.4625 0.86
25 SID 0.459459 0.82
26 SIA SIA SIA 0.453488 0.826923
27 MUS 0.449438 0.796296
28 NXD 0.447368 0.792453
29 WIA SIA 0.447059 0.767857
30 2FG SIA 0.447059 0.796296
31 KDO 0.435484 0.704545
32 NAG SIA 0.430233 0.781818
33 BND 0.416667 0.807692
34 SKD 0.414286 0.875
35 GAL SIA SIA 0.410526 0.811321
36 E3M 0.402778 0.606061
37 4AM 0.4 0.833333
38 DAN 0.4 0.911111
Similar Ligands (3D)
Ligand no: 1; Ligand: GAL SIA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 SIA GAL 0.9514
Ligand no: 2; Ligand: SIA; Similar ligands found: 27
No: Ligand Similarity coefficient
1 49A 0.9738
2 9AM 0.9671
3 DF4 0.9637
4 G28 0.9369
5 GC9 0.9014
6 G39 0.8962
7 9GW 0.8947
8 0HX 0.8920
9 ST5 0.8919
10 9GT 0.8895
11 K99 0.8872
12 ZMR 0.8860
13 2H8 0.8805
14 ST4 0.8777
15 R2D 0.8751
16 5M8 0.8749
17 9GN 0.8727
18 9GQ 0.8684
19 NG1 0.8662
20 KFN 0.8658
21 9GZ 0.8646
22 ST6 0.8636
23 LNV 0.8630
24 FID 0.8627
25 HBQ 0.8617
26 GYG 0.8600
27 RP6 0.8554
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4U60; 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: 1) in the query (biounit: 4u60.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4U60; Ligand: BGC GAL SIA NGA GAL; 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: 4u60.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4U60; Ligand: BGC GAL SIA NGA GAL; 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: 4u60.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4U60; Ligand: GAL SIA NGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4u60.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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