Receptor
PDB id Resolution Class Description Source Keywords
4MJ0 1.7 Å NON-ENZYME: OTHER BK POLYOMAVIRUS VP1 PENTAMER IN COMPLEX WITH GD3 OLIGOSACCHA BK POLYOMAVIRUS ANTIPARALLEL BETA SANDWICH JELLY-ROLL TOPOLOGY VIRAL PROTEPOLYOMAVIRUS RECEPTOR-SWITCHING GLYCAN RECEPTOR VIRUS MACAPSID PROTEIN ATTACHMENT TO HOST-CELL SURFACE RECEPTORS
Ref.: A STRUCTURE-GUIDED MUTATION IN THE MAJOR CAPSID PRO RETARGETS BK POLYOMAVIRUS. PLOS PATHOG. V. 9 03688 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL B:405;
C:405;
A:406;
E:403;
D:404;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL D:403;
C:404;
B:404;
E:402;
E:401;
A:405;
B:403;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SIA SIA I:1;
G:1;
Valid;
Valid;
none;
none;
submit data
598.511 n/a O=C(N...
BGC GAL SIA SIA F:1;
Valid;
none;
submit data
922.793 n/a O=C(N...
GAL SIA SIA H:1;
Valid;
none;
submit data
760.652 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MJ0 1.7 Å NON-ENZYME: OTHER BK POLYOMAVIRUS VP1 PENTAMER IN COMPLEX WITH GD3 OLIGOSACCHA BK POLYOMAVIRUS ANTIPARALLEL BETA SANDWICH JELLY-ROLL TOPOLOGY VIRAL PROTEPOLYOMAVIRUS RECEPTOR-SWITCHING GLYCAN RECEPTOR VIRUS MACAPSID PROTEIN ATTACHMENT TO HOST-CELL SURFACE RECEPTORS
Ref.: A STRUCTURE-GUIDED MUTATION IN THE MAJOR CAPSID PRO RETARGETS BK POLYOMAVIRUS. PLOS PATHOG. V. 9 03688 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4MJ0 - SIA 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: SIA SIA; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA 1 1
2 SLB SIA SIA 0.985915 1
3 SLB SIA SIA SIA SIA 0.985915 1
4 SIA SIA SIA SIA SIA SIA SIA 0.985915 1
5 SLB SIA SIA SIA 0.985915 1
6 SIA SIA SIA 0.717647 1
7 GAL SIA SIA 0.648936 0.981132
8 SIA CMO 0.64 0.87037
9 SIA 0.565789 0.826923
10 SLB 0.565789 0.826923
11 BGC GAL SIA SIA 0.554545 0.981132
12 MNA 0.544304 0.851852
13 GAL SIA NGA GAL SIA SIA 0.521368 0.981132
14 GAL NGA GAL SIA SIA 0.516949 0.981132
15 GAL SIA 0.516484 0.888889
16 2FG SIA 0.5 0.859649
17 BGC GAL SIA NGA SIA 0.495935 0.981132
18 NAG SIA 0.484536 0.910714
19 42D 0.464286 0.8
20 18D 0.464286 0.796296
21 CNP 0.45977 0.767857
22 MUS 0.456311 0.79661
23 GAL SIA NGA 0.449541 0.962264
24 CEQ BGC NGA GAL SIA SIA 0.448529 0.8
25 NGA GAL SIA 0.446429 0.980769
26 BGC CEQ GAL SLB NGA GAL SIA SIA 0.445255 0.83871
27 A2G GAL SIA 0.444444 0.962264
28 NGC 0.440476 0.811321
29 NGE 0.440476 0.811321
30 NAG GAL SIA 0.440367 0.962264
31 MN0 0.436782 0.818182
32 BGC GAL SIA 0.436364 0.907407
33 NAG 2FG SIA 0.428571 0.894737
34 GAL 5N6 0.423077 0.925926
35 SIA GAL NGA GAL 0.422414 0.962264
36 GAL SIA NGA GAL SIA 0.422414 0.962264
37 MAG FUC GAL SIA 0.420168 0.962264
38 NAG FUC GAL SIA 0.420168 0.962264
39 SID 0.417582 0.785714
40 MBG NGC 0.417476 0.907407
41 NGS GAL SIA 0.415254 0.761194
42 WIA SIA 0.411765 0.862069
43 GAL NAG GAL SIA 0.410256 0.944444
44 GAL SIA NGA GAL 0.410256 0.944444
45 GAL NGA GAL SIA 0.410256 0.962264
46 NXD 0.408602 0.793103
47 NDG GAL SIA SIA 0.40678 0.910714
48 NAG GAL SIA SIA 0.40678 0.944444
49 C5P SIA 0.406504 0.666667
50 425 0.405405 0.662338
51 NAG GAL NGC 0.401709 0.925926
52 GAL NAG FUC GAL SIA 0.4 0.962264
53 79J 0.4 0.849057
Ligand no: 2; Ligand: BGC GAL SIA SIA; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA SIA 1 1
2 GAL NGA GAL SIA SIA 0.909091 1
3 GAL SIA NGA GAL SIA SIA 0.786325 1
4 GAL NGA GAL SIA 0.781818 0.981132
5 BGC GAL SIA NGA SIA 0.77686 1
6 GAL SIA SIA 0.754717 1
7 GLC GAL NGC 0.743119 0.907407
8 BGC GAL SIA NGA GAL SIA 0.737288 0.981132
9 BGC GAL GLA NGA GAL SIA 0.731092 0.981132
10 NAG GAL SIA 0.724771 0.981132
11 GAL SIA NGA GAL SIA 0.675214 0.981132
12 BGC GAL SIA NGA GAL 0.674797 0.981132
13 BGC CEQ GAL SLB NGA GAL SIA SIA 0.671533 0.854839
14 A2G GAL SIA 0.669643 0.981132
15 NAG GAL NGC 0.666667 0.944444
16 BGC GAL SIA NAG 0.661157 0.981132
17 NGS GAL SIA 0.65 0.776119
18 NAG FUC GAL SIA 0.639344 0.981132
19 NGA GAL SIA 0.635593 0.962264
20 BGC GAL SIA NGA GAL FUC 0.631579 0.981132
21 GAL NAG FUC GAL SIA 0.622047 0.981132
22 BGC GAL SIA 0.615385 0.925926
23 NAG GAL SIA SIA 0.614754 0.962963
24 MAG FUC GAL SIA 0.612903 0.944444
25 SIA GAL NGA GAL 0.606557 0.981132
26 NDG GAL SIA SIA 0.601626 0.928571
27 CEQ BGC NGA GAL SIA SIA 0.594406 0.815385
28 NGS FUC GLA SIA 0.590909 0.776119
29 BGC GAL NAG GAL SIA 0.587786 0.962963
30 NAG GAL PKM 0.577236 0.962963
31 GAL SIA NGA 0.575 0.981132
32 SLB SIA SIA 0.563636 0.981132
33 SLB SIA SIA SIA SIA 0.563636 0.981132
34 SIA SIA SIA SIA SIA SIA SIA 0.563636 0.981132
35 SLB SIA SIA SIA 0.563636 0.981132
36 2FG SIA 0.5625 0.877193
37 BGC 16C GAL SIA 0.5625 0.854839
38 SIA SIA 0.554545 0.981132
39 SIA SIA SIA 0.552632 0.981132
40 BGC 18C GAL SIA 0.544218 0.854839
41 GAL SIA NGA GAL 0.543307 0.962963
42 GAL 5N6 0.543103 0.944444
43 NAG 2FG SIA 0.540323 0.912281
44 MBG NGC 0.53913 0.890909
45 NGA POL GAL NGC AZI 0.537313 0.772727
46 Z3Q GAL 5N6 0.533835 0.825397
47 NAG GAL NAG GAL SIA 0.510949 0.962963
48 GAL NAG GAL SIA 0.484848 0.962963
49 BGC 18C GAL SIA NGA GAL 0.461078 0.854839
50 NAG GAL 5N6 0.459259 0.945455
51 SIA CMO 0.439252 0.854545
52 GAL SIA 0.432203 0.907407
53 BGC GAL NAG 0.410256 0.849057
54 BGC GAL NAG GAL 0.403361 0.849057
Ligand no: 3; Ligand: GAL SIA SIA; Similar ligands found: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL SIA SIA 1 1
2 BGC GAL SIA SIA 0.754717 1
3 GAL SIA NGA GAL SIA SIA 0.723214 1
4 GAL NGA GAL SIA SIA 0.701754 1
5 GAL 5N6 0.697917 0.944444
6 2FG SIA 0.673684 0.877193
7 SLB SIA SIA SIA 0.659574 0.981132
8 SIA SIA SIA SIA SIA SIA SIA 0.659574 0.981132
9 SLB SIA SIA SIA SIA 0.659574 0.981132
10 SLB SIA SIA 0.659574 0.981132
11 SIA SIA 0.648936 0.981132
12 A2G GAL SIA 0.628571 0.981132
13 SIA SIA SIA 0.626263 0.981132
14 BGC GAL SIA NGA SIA 0.617886 1
15 NAG GAL SIA 0.607477 0.981132
16 GAL SIA NGA GAL SIA 0.607143 0.981132
17 GAL NAG FUC GAL SIA 0.596639 0.981132
18 GAL SIA NGA 0.587156 0.981132
19 NGA GAL SIA 0.580357 0.962264
20 GAL NGA GAL SIA 0.578947 0.981132
21 BGC CEQ GAL SLB NGA GAL SIA SIA 0.577778 0.854839
22 NAG FUC GAL SIA 0.57265 0.981132
23 NGS GAL SIA 0.568965 0.776119
24 SIA GAL NGA GAL 0.565217 0.981132
25 MBG NGC 0.563107 0.890909
26 NAG 2FG SIA 0.5625 0.912281
27 NAG GAL SIA SIA 0.560345 0.962963
28 NAG GAL NGC 0.556522 0.944444
29 NDG GAL SIA SIA 0.547009 0.928571
30 MAG FUC GAL SIA 0.546219 0.944444
31 BGC GAL GLA NGA GAL SIA 0.544715 0.981132
32 NGS FUC GLA SIA 0.539683 0.776119
33 BGC GAL SIA NGA GAL SIA 0.536585 0.981132
34 CEQ BGC NGA GAL SIA SIA 0.536232 0.815385
35 GLC GAL NGC 0.526316 0.907407
36 SIA CMO 0.516484 0.854545
37 GAL SIA NGA GAL 0.512605 0.962963
38 BGC GAL SIA NAG 0.504065 0.981132
39 GAL NAG GAL SIA 0.5 0.962963
40 GAL SIA 0.5 0.907407
41 BGC GAL SIA NGA GAL 0.496063 0.981132
42 BGC GAL SIA NGA GAL FUC 0.488889 0.981132
43 NGA POL GAL NGC AZI 0.484375 0.772727
44 BGC GAL SIA 0.478632 0.925926
45 NAG GAL PKM 0.471074 0.962963
46 Z3Q GAL 5N6 0.46875 0.825397
47 BGC 16C GAL SIA 0.461538 0.854839
48 MNA 0.457447 0.836364
49 BGC 18C GAL SIA 0.455172 0.854839
50 NAG SIA 0.445455 0.928571
51 BGC GAL NAG GAL SIA 0.422222 0.962963
52 NAG GAL NAG GAL SIA 0.414815 0.962963
53 SLB 0.410526 0.811321
54 SIA 0.410526 0.811321
Similar Ligands (3D)
Ligand no: 1; Ligand: SIA SIA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 SLB SIA 0.8744
Ligand no: 2; Ligand: BGC GAL SIA SIA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 3; Ligand: 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 : 4MJ0; Ligand: 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: 4mj0.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4MJ0; Ligand: 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: 4mj0.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4MJ0; Ligand: 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: 3) in the query (biounit: 4mj0.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4MJ0; Ligand: BGC 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: 4) in the query (biounit: 4mj0.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
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