Receptor
PDB id Resolution Class Description Source Keywords
1VPS 1.9 Å NON-ENZYME: TOXIN_VIRAL POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXA MURINE POLYOMAVIRUS VIRUS COAT PROTEIN OLIGOSACCHARIDE BINDING VIRUS ASSEMBLYACID VIRAL PROTEIN
Ref.: HIGH-RESOLUTION STRUCTURE OF A POLYOMAVIRUS VP1-OLIGOSACCHARIDE COMPLEX: IMPLICATIONS FOR ASSEM RECEPTOR BINDING. EMBO J. V. 16 5139 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG GAL SIA SIA F:1;
G:1;
J:1;
H:1;
I:1;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
963.846 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CPZ 1.71 Å NON-ENZYME: TOXIN_VIRAL CRYSTAL STRUCTURE OF MURINE POLYOMAVIRUS RA STRAIN VP1 IN CO THE GT1A GLYCAN MURINE POLYOMAVIRUS (STRAIN P16 SMALL-ORGANISM_COMMON: MPYV MURINE POLYOMAVIRUS VIRUS PROTEIN CARBOHYDRATE COMPLEX VIINTERACTION VIRAL PROTEIN
Ref.: STRUCTURAL AND FUNCTIONAL ANALYSIS OF MURINE POLYOM CAPSID PROTEINS ESTABLISH THE DETERMINANTS OF LIGAN RECOGNITION AND PATHOGENICITY. PLOS PATHOG. V. 11 05104 2015
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 64 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
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: NAG GAL SIA SIA; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL SIA SIA 1 1
2 A2G GAL SIA 0.838384 0.981132
3 NDG GAL SIA SIA 0.745455 0.963636
4 NGA GAL SIA 0.740741 0.962264
5 NAG GAL SIA 0.71028 0.981132
6 NAG FUC GAL SIA 0.695652 0.981132
7 GAL NGA GAL SIA 0.690265 0.981132
8 GAL SIA NGA GAL SIA 0.690265 0.981132
9 NGS GAL SIA 0.678261 0.776119
10 NGS FUC GLA SIA 0.666667 0.776119
11 NAG 2FG SIA 0.660714 0.912281
12 NAG GAL NGC 0.652174 0.944444
13 GAL NAG GAL SIA 0.646552 1
14 BGC GAL SIA NGA GAL SIA 0.639344 0.981132
15 BGC GAL GLA NGA GAL SIA 0.634146 0.981132
16 MAG FUC GAL SIA 0.625 0.944444
17 GAL SIA NGA GAL SIA SIA 0.619048 0.962963
18 BGC GAL SIA SIA 0.614754 0.962963
19 GAL NGA GAL SIA SIA 0.614173 0.962963
20 BGC GAL SIA 0.614035 0.962264
21 GAL NAG FUC GAL SIA 0.608 0.981132
22 SIA GAL NGA GAL 0.605042 0.981132
23 NAG GAL NAG GAL SIA 0.603175 1
24 NGA POL GAL NGC AZI 0.595238 0.772727
25 GLC GAL NGC 0.594828 0.907407
26 GAL SIA NGA GAL 0.591667 1
27 2FG SIA 0.588785 0.877193
28 BGC GAL NAG GAL SIA 0.585938 1
29 BGC GAL SIA NGA GAL 0.582677 0.981132
30 GAL 5N6 0.567568 0.944444
31 Z3Q GAL 5N6 0.566929 0.825397
32 MBG NGC 0.563636 0.890909
33 NAG GAL PKM 0.561983 0.962963
34 GAL SIA 0.561905 0.943396
35 NAG GAL 5N6 0.560976 0.981481
36 GAL SIA SIA 0.560345 0.962963
37 GAL SIA NGA 0.546219 0.981132
38 BGC GAL SIA NAG 0.53125 0.981132
39 BGC GAL SIA NGA GAL FUC 0.514286 0.981132
40 BGC CEQ GAL SLB NGA GAL SIA SIA 0.513514 0.825397
41 NAG SIA 0.504425 0.928571
42 BGC 16C GAL SIA 0.496599 0.854839
43 BGC 18C GAL SIA 0.489933 0.854839
44 BGC GAL SIA NGA SIA 0.478873 0.962963
45 SIA CMO 0.460784 0.854545
46 BGC 18C GAL SIA NGA GAL 0.431138 0.854839
47 C4W NAG FUC BMA MAN NAG GAL SIA 0.43038 0.868852
48 A2G THR ALA PRO GLY GLY NAG SIA 0.423529 0.768116
49 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.422619 0.868852
50 CEQ BGC NGA GAL SIA SIA 0.420382 0.815385
51 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.416107 0.963636
52 MNA 0.409524 0.836364
53 SIA SIA 0.40678 0.944444
54 SLB SIA SIA SIA SIA 0.403361 0.944444
55 SIA SIA SIA SIA SIA SIA SIA 0.403361 0.944444
56 SLB SIA SIA 0.403361 0.944444
57 SLB SIA SIA SIA 0.403361 0.944444
Similar Ligands (3D)
Ligand no: 1; Ligand: NAG GAL SIA SIA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CPZ; Ligand: GAL NGA GAL SIA 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: 5cpz.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5CPZ; Ligand: GAL NGA GAL SIA SIA; 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: 5cpz.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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