Receptor
PDB id Resolution Class Description Source Keywords
4MBY 1.48 Å NON-ENZYME: OTHER STRUCTURE OF B-LYMPHOTROPIC POLYOMAVIRUS VP1 IN COMPLEX WITH SIALYLLACTOSE B-LYMPHOTROPIC POLYOMAVIRUS JELLY ROLL POLYOMAVIRUS VIRAL CAPSID (STRUCTURAL) PROTEINENCAPSIDATION RECEPTOR BINDING SIALYLATED OLIGOSACCHARIDEPROTEIN
Ref.: STRUCTURES OF B-LYMPHOTROPIC POLYOMAVIRUS VP1 IN CO WITH OLIGOSACCHARIDE LIGANDS. PLOS PATHOG. V. 9 03714 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA D:401;
G:401;
A:401;
I:401;
E:401;
C:401;
F:401;
J:401;
B:401;
H:401;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
EDO A:403;
A:404;
E:406;
B:404;
A:405;
B:406;
B:407;
A:406;
D:403;
C:404;
F:403;
G:403;
B:405;
B:403;
E:403;
H:404;
E:405;
C:405;
G:404;
I:403;
J:403;
J:406;
I:404;
H:405;
A:407;
E:404;
C:403;
H:403;
J:405;
B:408;
J:404;
D:404;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CL A:402;
G:402;
E:402;
F:402;
B:402;
I:402;
H:402;
D:402;
J:402;
C:402;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
IPA G:405;
H:406;
B:409;
F:404;
C:406;
E:407;
J:407;
I:405;
A:408;
D:405;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
60.095 C3 H8 O CC(C)...
GAL SIA N:1;
O:1;
P:1;
M:1;
L:1;
K:1;
Q:1;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
454.405 n/a O=C(N...
BGC GAL SIA R:1;
S:1;
 Valid;
Valid;
 none;
none;
 submit data
632.545 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4MBY 1.48 Å NON-ENZYME: OTHER STRUCTURE OF B-LYMPHOTROPIC POLYOMAVIRUS VP1 IN COMPLEX WITH SIALYLLACTOSE B-LYMPHOTROPIC POLYOMAVIRUS JELLY ROLL POLYOMAVIRUS VIRAL CAPSID (STRUCTURAL) PROTEINENCAPSIDATION RECEPTOR BINDING SIALYLATED OLIGOSACCHARIDEPROTEIN
Ref.: STRUCTURES OF B-LYMPHOTROPIC POLYOMAVIRUS VP1 IN CO WITH OLIGOSACCHARIDE LIGANDS. PLOS PATHOG. V. 9 03714 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 4MBY - GAL SIA n/a n/a
2 4MBZ - 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: BGC GAL SIA; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA 1 1
2 BGC GAL NAG GAL SIA 0.82243 0.962264
3 NAG GAL 5N6 0.719626 0.944444
4 NAG GAL NAG GAL SIA 0.716814 0.962264
5 GAL NAG GAL SIA 0.694444 0.962264
6 BGC GAL SIA NGA GAL 0.649573 0.943396
7 GAL NGA GAL SIA 0.648649 0.943396
8 BGC GAL SIA NAG 0.634783 0.943396
9 BGC GAL GLA NGA GAL SIA 0.621849 0.943396
10 BGC GAL SIA SIA 0.615385 0.925926
11 NAG GAL SIA SIA 0.614035 0.962264
12 BGC GAL SIA NGA GAL SIA 0.613445 0.943396
13 GAL SIA 0.608247 0.980392
14 GLC GAL NGC 0.594595 0.942308
15 SIA GAL NGA GAL 0.591304 0.943396
16 BGC GAL SIA NGA GAL FUC 0.581395 0.943396
17 NAG GAL SIA 0.576577 0.943396
18 GAL NGA GAL SIA SIA 0.576 0.925926
19 NDG GAL SIA SIA 0.57265 0.927273
20 C4W NAG FUC BMA MAN NAG GAL SIA 0.568345 0.836066
21 BGC GAL SIA NGA SIA 0.565891 0.925926
22 GAL SIA NGA 0.557522 0.943396
23 NAG SIA 0.542857 0.892857
24 GAL SIA NGA GAL 0.537815 0.962264
25 GAL SIA NGA GAL SIA 0.537815 0.943396
26 NAG GAL NGC 0.529412 0.943396
27 NGS GAL SIA 0.528926 0.746269
28 A2G GAL SIA 0.526316 0.943396
29 NAG FUC GAL SIA 0.520325 0.943396
30 C4W NAG FUC BMA MAN MAN NAG GAL SIA NAG 0.519737 0.836066
31 2FG SIA 0.514019 0.909091
32 SIA CMO 0.5 0.851852
33 GAL NAG FUC GAL SIA 0.496124 0.943396
34 NAG 2FG SIA 0.495798 0.877193
35 NGS FUC GLA SIA 0.492424 0.746269
36 NGA GAL SIA 0.487603 0.924528
37 GAL SIA NGA GAL SIA SIA 0.484848 0.925926
38 MAG FUC GAL SIA 0.484127 0.907407
39 NAG GAL PKM 0.483607 0.925926
40 GAL SIA SIA 0.478632 0.925926
41 GAL 1GN BGC ACY GAL 1GN BGC ACY GAL 6PZ 0.460432 0.927273
42 GAL 5N6 0.45614 0.943396
43 BGC 16C GAL SIA 0.452055 0.822581
44 BGC GAL NGA GAL 0.447619 0.882353
45 MNA 0.443299 0.833333
46 GLC GLC FRU 0.442308 0.648148
47 BGC GAL NAG GAL 0.439252 0.882353
48 MBG NGC 0.438596 0.924528
49 BGC GAL NGA 0.436893 0.882353
50 SIA SIA 0.436364 0.907407
51 BGC 18C GAL SIA 0.436242 0.822581
52 WIA SIA 0.433628 0.910714
53 SLB SIA SIA SIA SIA 0.432432 0.907407
54 SLB SIA SIA SIA 0.432432 0.907407
55 SIA SIA SIA SIA SIA SIA SIA 0.432432 0.907407
56 SLB SIA SIA 0.432432 0.907407
57 BGC CEQ GAL SLB NGA GAL SIA SIA 0.430464 0.793651
58 NGA POL GAL NGC AZI 0.42963 0.769231
59 NAG G6S 0.428571 0.738462
60 SIA SIA SIA 0.426087 0.907407
61 CEQ BGC NGA GAL SIA SIA 0.423841 0.784615
62 BGC GAL NAG NAG GAL GAL 0.423729 0.867925
63 BGC GAL GLA NGA GAL 0.423423 0.882353
64 A2G THR ALA PRO GLY GLY NAG SIA 0.418182 0.73913
65 GLY PRO ALA THR PRO ALA PRO A2G SIA 0.417722 0.73913
66 BGC 18C GAL SIA NGA GAL 0.417178 0.822581
67 Z3Q GAL 5N6 0.414815 0.793651
68 BGC GLC GLC 0.41 0.647059
69 BGC GAL NAG 0.407407 0.882353
70 C5P SIA 0.404412 0.675676
71 BGC GAL GLA NGA 0.401786 0.882353
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: BGC GAL SIA; Similar ligands found: 2
No: Ligand Similarity coefficient
1 GLC GLA SIA 0.9909
2 GLC GAL SIA 0.9887
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MBY; Ligand: BGC GAL 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: 4mby.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4MBY; Ligand: BGC GAL 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: 4mby.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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