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
SIA GAL NAG SIA A:1;
B:1;
C:1;
D:1;
E:1;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
963.846 n/a O=C([...
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 60 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
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 NAG SIA; Similar ligands found: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL NAG SIA 1 1
2 SIA GAL A2G 0.838384 0.981132
3 NGA GAL SIA 0.838384 0.981132
4 SIA GAL NDG SIA 0.745455 0.963636
5 NAG SIA GAL 0.71028 0.981132
6 SIA GAL NAG 0.71028 0.981132
7 FUC NDG GAL SIA 0.695652 0.981132
8 SIA GAL NAG FUC 0.695652 0.981132
9 NDG FUC SIA GAL 0.695652 0.981132
10 SIA GLA NAG FUC 0.695652 0.981132
11 NAG FUC SIA GAL 0.695652 0.981132
12 SIA GAL NDG FUC 0.695652 0.981132
13 BGC GAL SIA 0.694444 0.943396
14 BGC SIA GAL 0.694444 0.943396
15 SIA GAL BGC 0.694444 0.943396
16 GAL BGC SIA 0.694444 0.943396
17 GLA GLC SIA 0.694444 0.943396
18 SIA GAL GLC 0.694444 0.943396
19 SIA BGC GAL 0.694444 0.943396
20 GAL SIA NGA GAL SIA 0.690265 0.981132
21 SIA GAL NGA GAL 0.690265 0.981132
22 GAL NGA GAL SIA 0.690265 0.981132
23 SIA GAL NGS 0.663793 0.8
24 SIA 2FG NAG 0.660714 0.912281
25 SIA GLA NGS FUC 0.653226 0.8
26 NAG GAL NGC 0.652174 0.944444
27 SIA NAG GAL GAL 0.646552 1
28 BGC GAL SIA SIA GAL NGA 0.639344 0.981132
29 GAL BGC GAL SIA NGA SIA 0.639344 0.981132
30 SIA GAL 0.637255 0.943396
31 GAL TNR SIA 0.632479 0.981481
32 SIA GAL MAG FUC 0.625 0.944444
33 NAG GAL SIA 0.622807 1
34 SIA SIA GAL NGA GAL SIA 0.619048 0.962963
35 SIA SIA GLA BGC 0.614754 0.962963
36 BGC SIA SIA GAL 0.614754 0.962963
37 SIA SIA GAL NGA GAL 0.614173 0.962963
38 GAL SIA NGA GAL 0.605042 0.981132
39 SIA NAG GAL 0.603448 0.963636
40 GAL SIA 0.596154 0.962264
41 NGC GAL NGA POL AZI 0.595238 0.772727
42 MN0 GAL GLC 0.594828 0.907407
43 SIA 2FG 0.588785 0.877193
44 4U2 0.587719 0.962264
45 SIA GAL NAG GAL GLC 0.585938 1
46 BGC GAL NAG SIA GAL 0.585938 1
47 SIA GAL NAG GAL BGC 0.585938 1
48 GAL NGA SIA GAL BGC 0.582677 0.981132
49 GAL NGA GAL BGC SIA 0.582677 0.981132
50 BGC GAL SIA NGA GAL 0.582677 0.981132
51 SIA GAL BGC NGA GAL 0.582677 0.981132
52 BGC GAL SIA NGA GAL SIA 0.576642 0.83871
53 SLT 0.573913 0.924528
54 GAL NAG SIA GAL 0.572581 1
55 SIA GAL NAG GAL 0.572581 1
56 5N6 GAL 0.567568 0.944444
57 Z3Q GAL 5N6 0.566929 0.825397
58 NGC MBG 0.563636 0.890909
59 SIA SIA GAL 0.560345 0.962963
60 SIA GAL NGA 0.546219 0.981132
61 BGC GAL SIA NGA 0.53125 0.981132
62 GAL BGC SIA NGA 0.53125 0.981132
63 SIA GAL BGC NGA 0.53125 0.981132
64 4U1 0.516393 0.981132
65 BGC GAL CEQ SLB NGA GAL SIA SIA 0.513514 0.852459
66 4U0 0.508197 0.943396
67 SIA NAG 0.504425 0.928571
68 SIA GAL BGC 16C 0.496599 0.854839
69 BGC 18C GAL SIA 0.489933 0.854839
70 SIA GAL SIA BGC NGA 0.478873 0.962963
71 SIA GAL SIA GLC NGA 0.478873 0.962963
72 SIA CMO 0.460784 0.854545
73 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.455172 0.981481
74 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.455172 0.981481
75 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.432432 0.981481
76 BGC 18C GAL NGA SIA GAL 0.431138 0.854839
77 A2G THR ALA PRO GLY GLY NAG SIA 0.423529 0.779412
78 SIA GAL SIA BGC NGA CEQ 0.420382 0.815385
79 MNA 0.409524 0.836364
80 SLB SIA 0.40678 0.944444
81 SIA SIA 0.40678 0.944444
82 SIA SIA SIA SLB 0.403361 0.944444
83 SIA SIA SIA SIA SIA SIA SIA 0.403361 0.944444
84 SLB SIA SIA 0.403361 0.944444
85 SLB SIA SIA SIA SIA 0.403361 0.944444
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CPZ; Ligand: SIA SIA GAL NGA GAL; Similar sites found: 12
This union binding pocket(no: 1) in the query (biounit: 5cpz.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GDN FAD 0.02076 0.42722 2.46479
2 3GDN HBX 0.02708 0.42722 2.46479
3 3QVP FAD 0.01019 0.4448 2.8169
4 4ZSD 7I6 0.01536 0.40316 3.04878
5 1GPE FAD 0.009349 0.44856 3.16901
6 3P8N L4T 0.018 0.4101 4.30108
7 2IO8 ADP 0.0242 0.40356 4.57746
8 5NB7 8NQ 0.02343 0.40276 4.78261
9 3V4S ADP 0.03762 0.40581 4.92958
10 1KJ8 GAR 0.0343 0.40996 5.6338
11 1AFS NAP 0.03683 0.40194 6.33803
12 2R75 01G 0.0346 0.40097 6.33803
Pocket No.: 2; Query (leader) PDB : 5CPZ; Ligand: SIA SIA GAL NGA GAL; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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