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-]
SIA GAL D:406;
A:409;
G:406;
C:407;
E:408;
B:410;
H:407;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
submit data
470.404 n/a O=C([...
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)...
BGC SIA GAL I:407;
J:409;
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 1579 families.
1 4MBY - SIA GAL n/a n/a
2 4MBZ - SIA GAL 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 45 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 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 - SIA GAL GLC n/a n/a
12 4POR - BGC SIA GAL n/a n/a
13 4POS - NAG SIA GAL n/a n/a
14 4POT - NAG GAL NGC n/a n/a
15 4MJ0 - BGC SIA SIA GAL n/a n/a
16 3NXD - BGC GAL NAG SIA GAL n/a n/a
17 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
18 4X15 - SIA GAL BGC NGA n/a n/a
19 4X10 - SIA GAL BGC NGA n/a n/a
20 4X0Z - SIA GAL BGC NGA GAL n/a n/a
21 4X17 - SIA SIA n/a n/a
22 4JCF - SIA GAL NAG n/a n/a
23 4X12 - SIA SIA n/a n/a
24 4X14 - SIA GAL BGC NGA GAL n/a n/a
25 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
26 4X13 - SIA GAL NAG GAL BGC n/a n/a
27 4MBY - SIA GAL n/a n/a
28 4MBZ - SIA GAL n/a n/a
29 4FMI - NAG SIA GAL n/a n/a
30 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
31 4FMH - SIA GAL n/a n/a
50% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 37 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 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 - SIA GAL GLC n/a n/a
12 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
13 4POR - BGC SIA GAL n/a n/a
14 4POS - NAG SIA GAL n/a n/a
15 4POT - NAG GAL NGC n/a n/a
16 4MJ0 - BGC SIA SIA GAL n/a n/a
17 3NXD - BGC GAL NAG SIA GAL n/a n/a
18 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
19 4X15 - SIA GAL BGC NGA n/a n/a
20 4X10 - SIA GAL BGC NGA n/a n/a
21 4X0Z - SIA GAL BGC NGA GAL n/a n/a
22 4X17 - SIA SIA n/a n/a
23 4JCF - SIA GAL NAG n/a n/a
24 4X12 - SIA SIA n/a n/a
25 4X14 - SIA GAL BGC NGA GAL n/a n/a
26 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
27 4X13 - SIA GAL NAG GAL BGC n/a n/a
28 4MBY - SIA GAL n/a n/a
29 4MBZ - SIA GAL n/a n/a
30 4FMI - NAG SIA GAL n/a n/a
31 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
32 4FMH - SIA GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA GAL; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL 1 1
2 GAL SIA 1 1
3 SIA SIA GAL 0.835294 0.943396
4 SIA 2FG 0.790123 0.925926
5 SIA GAL A2G 0.725275 0.961538
6 NGA GAL SIA 0.725275 0.961538
7 GAL BGC SIA 0.717391 1
8 GLA GLC SIA 0.717391 1
9 SIA GAL GLC 0.717391 1
10 BGC SIA GAL 0.717391 1
11 SIA GAL BGC 0.717391 1
12 BGC GAL SIA 0.717391 1
13 NAG SIA GAL 0.698925 0.961538
14 GAL SIA NGA GAL SIA 0.676768 0.961538
15 SIA GAL NGA 0.65625 0.961538
16 NGC MBG 0.651685 0.942308
17 NAG GAL FUC GAL SIA 0.64486 0.961538
18 SIA 2FG NAG 0.642857 0.892857
19 SIA GAL NAG GAL 0.64 0.943396
20 SIA GAL NAG SIA 0.637255 0.943396
21 NAG GAL NGC 0.633663 0.961538
22 SIA GAL NGS 0.631068 0.757576
23 GAL SIA NGA GAL 0.627451 0.961538
24 SIA GAL NGA GAL 0.627451 0.961538
25 SIA SIA GLA BGC 0.622642 0.943396
26 BGC SIA SIA GAL 0.622642 0.943396
27 SIA GAL NDG SIA 0.621359 0.909091
28 SIA GAL NAG FUC 0.619048 0.961538
29 NDG FUC SIA GAL 0.619048 0.961538
30 FUC NDG GAL SIA 0.619048 0.961538
31 NAG FUC SIA GAL 0.619048 0.961538
32 SIA GAL NDG FUC 0.619048 0.961538
33 SIA GLA NAG FUC 0.619048 0.961538
34 SIA GAL NGA GLA GAL BGC 0.614679 0.961538
35 BGC GAL SIA NGA GAL SIA 0.605505 0.961538
36 BGC GAL SIA SIA GAL NGA 0.605505 0.961538
37 MN0 GAL GLC 0.6 0.960784
38 SIA SIA GAL NGA GAL SIA 0.598214 0.943396
39 SIA GAL MAG FUC 0.588785 0.924528
40 GAL NGA GAL SIA 0.580952 0.943396
41 SIA SIA GAL NGA GAL 0.578947 0.943396
42 SLT 0.575758 0.98
43 SIA GAL BGC NGA 0.568807 0.961538
44 GAL BGC SIA NGA 0.568807 0.961538
45 NAG GAL BGC SIA 0.568807 0.961538
46 BGC GAL SIA NGA 0.568807 0.961538
47 SIA NAG GAL GAL 0.566038 0.943396
48 SIA GLA NGS FUC 0.565217 0.757576
49 4U2 0.56 0.942308
50 BGC GAL SIA NGA GAL 0.557522 0.961538
51 GAL NGA SIA GAL BGC 0.557522 0.961538
52 GAL NGA GAL BGC SIA 0.557522 0.961538
53 SIA GAL BGC NGA GAL 0.557522 0.961538
54 GAL NAG SIA GAL 0.545455 0.943396
55 NGC GAL NGA POL AZI 0.54386 0.78125
56 MNA 0.5375 0.849057
57 SIA NAG GAL 0.533333 0.909091
58 NAG GAL SIA 0.52381 0.943396
59 SIA GAL NAG 0.52381 0.943396
60 SIA GAL BGC NGA GAL FUC 0.520325 0.961538
61 SLB SIA 0.516129 0.924528
62 SIA SIA 0.516129 0.924528
63 SLB SIA SIA 0.510638 0.924528
64 SIA SIA SIA SIA SIA SIA SIA 0.510638 0.924528
65 SIA NAG 0.510417 0.875
66 SIA GAL SIA BGC NGA 0.504065 0.943396
67 SIA GAL SIA GLC NGA 0.504065 0.943396
68 GAL TNR SIA 0.491071 0.909091
69 SIA GAL BGC 16C 0.48855 0.806452
70 4U0 0.485981 0.960784
71 SIA SIA SIA 0.484848 0.924528
72 BGC 18C GAL SIA 0.481203 0.806452
73 BGC GAL CEQ SLB NGA GAL SIA SIA 0.474074 0.806452
74 BGC GAL NAG SIA GAL 0.471074 0.943396
75 SIA GAL NAG GAL GLC 0.471074 0.943396
76 SIA GAL NAG GAL BGC 0.471074 0.943396
77 4U1 0.46789 0.924528
78 SLB 0.463415 0.86
79 SIA 0.463415 0.86
80 SIA WIA 0.45 0.892857
81 CNP 0.438202 0.796296
82 SIA GAL SIA BGC NGA CEQ 0.434783 0.769231
83 MN0 0.431818 0.849057
84 SID 0.413043 0.781818
85 MUS 0.411215 0.793103
86 NXD 0.404255 0.789474
87 C5P SIA 0.403226 0.684932
Ligand no: 2; Ligand: BGC SIA GAL; Similar ligands found: 98
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA 1 1
2 GLA GLC SIA 1 1
3 GAL BGC SIA 1 1
4 BGC SIA GAL 1 1
5 SIA GAL GLC 1 1
6 SIA GAL BGC 1 1
7 SIA SIA GLA BGC 0.861386 0.943396
8 BGC SIA SIA GAL 0.861386 0.943396
9 MN0 GAL GLC 0.852632 0.960784
10 BGC GAL SIA NGA GAL SIA 0.836538 0.961538
11 BGC GAL SIA SIA GAL NGA 0.836538 0.961538
12 NAG SIA GAL 0.831579 0.961538
13 SLT 0.829787 0.98
14 SIA GAL NGA GLA GAL BGC 0.828571 0.961538
15 SIA SIA GAL NGA GAL 0.781818 0.943396
16 SIA GAL A2G 0.765306 0.961538
17 NGA GAL SIA 0.765306 0.961538
18 GAL NGA GAL BGC SIA 0.761468 0.961538
19 GAL NGA SIA GAL BGC 0.761468 0.961538
20 SIA GAL BGC NGA GAL 0.761468 0.961538
21 BGC GAL SIA NGA GAL 0.761468 0.961538
22 NAG GAL NGC 0.757282 0.961538
23 GAL SIA NGA GAL SIA 0.75 0.961538
24 SIA GAL BGC NGA 0.747664 0.961538
25 BGC GAL SIA NGA 0.747664 0.961538
26 GAL BGC SIA NGA 0.747664 0.961538
27 NAG GAL BGC SIA 0.747664 0.961538
28 SIA GAL NGS 0.719626 0.757576
29 GAL SIA 0.717391 1
30 SIA GAL 0.717391 1
31 SIA GAL NAG GAL 0.698113 0.943396
32 SIA GAL NAG SIA 0.694444 0.943396
33 SIA GAL NAG FUC 0.690909 0.961538
34 NDG FUC SIA GAL 0.690909 0.961538
35 NAG FUC SIA GAL 0.690909 0.961538
36 SIA GLA NAG FUC 0.690909 0.961538
37 FUC NDG GAL SIA 0.690909 0.961538
38 SIA GAL NDG FUC 0.690909 0.961538
39 4U2 0.686275 0.942308
40 SIA GAL NDG SIA 0.678899 0.909091
41 SIA GAL BGC NGA GAL FUC 0.677686 0.961538
42 GAL SIA NGA GAL 0.669725 0.961538
43 SIA GAL NGA GAL 0.669725 0.961538
44 NAG GAL FUC GAL SIA 0.669565 0.961538
45 SIA SIA GAL NGA GAL SIA 0.666667 0.943396
46 SIA GAL SIA GLC NGA 0.661157 0.943396
47 SIA GAL SIA BGC NGA 0.661157 0.943396
48 SIA GAL MAG FUC 0.660714 0.924528
49 SIA GAL NAG GAL GLC 0.65812 0.943396
50 SIA GAL NAG GAL BGC 0.65812 0.943396
51 BGC GAL NAG SIA GAL 0.65812 0.943396
52 SIA 2FG 0.642857 0.925926
53 4U0 0.635514 0.960784
54 SIA GAL NGA 0.635514 0.961538
55 SIA SIA GAL 0.622642 0.943396
56 SIA GLA NGS FUC 0.619835 0.757576
57 NGC MBG 0.613861 0.942308
58 GAL NGA GAL SIA 0.610619 0.943396
59 SIA 2FG NAG 0.609091 0.892857
60 NGC GAL NGA POL AZI 0.6 0.78125
61 SIA GAL BGC 16C 0.598485 0.806452
62 NAG GAL SIA 0.585586 0.943396
63 SIA GAL NAG 0.585586 0.943396
64 BGC 18C GAL SIA 0.577778 0.806452
65 BGC GAL CEQ SLB NGA GAL SIA SIA 0.569343 0.806452
66 SIA NAG GAL 0.552632 0.909091
67 GAL NAG SIA GAL 0.55 0.943396
68 SIA NAG GAL GAL 0.542373 0.943396
69 4U1 0.530435 0.924528
70 GAL TNR SIA 0.512397 0.909091
71 SIA GAL SIA BGC NGA CEQ 0.496504 0.769231
72 BGC 18C GAL NGA SIA GAL 0.483871 0.806452
73 NAG GAL BGC 0.466019 0.9
74 LAT NAG GAL 0.462264 0.9
75 GLC GAL NAG GAL 0.462264 0.9
76 GAL NAG GAL GLC 0.457143 0.9
77 BGC GAL NAG GAL 0.457143 0.9
78 MNA 0.447917 0.849057
79 NGA GLA GAL BGC 0.444444 0.9
80 GAL NGA GLA BGC GAL 0.440367 0.9
81 SIA SIA 0.440367 0.924528
82 SLB SIA 0.440367 0.924528
83 SIA NAG 0.4375 0.875
84 SIA SIA SIA SIA SIA SIA SIA 0.436364 0.924528
85 SLB SIA SIA 0.436364 0.924528
86 SIA SIA SIA 0.429825 0.924528
87 NGA GAL BGC 0.413462 0.9
88 SIA WIA 0.412281 0.892857
89 FUC GAL NAG GAL BGC 0.40678 0.882353
90 GAL GLC NAG GAL FUC 0.40678 0.882353
91 GLC NAG GAL GAL FUC 0.40678 0.882353
92 BGC GAL NAG GAL FUC FUC 0.404959 0.901961
93 GLC GAL NAG GAL FUC FUC 0.404959 0.901961
94 GAL BGC NAG NAG GAL GAL 0.403361 0.884615
95 MUS 0.403361 0.793103
96 SLB 0.402062 0.86
97 GLA GAL GAL 0.402062 0.66
98 SIA 0.402062 0.86
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4MBY; Ligand: BGC SIA GAL; 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 SIA 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: 4mby.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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