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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
454.405 n/a O=C(N...
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 1443 families.
1 4MBY - SIA GAL n/a n/a
2 4MBZ - SIA GAL n/a n/a
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 43 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 4X17 - SIA SIA n/a n/a
20 4JCF - SIA GAL NAG n/a n/a
21 4X12 - SIA SIA n/a n/a
22 4X14 - SIA GAL BGC NGA GAL n/a n/a
23 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
24 4X13 - SIA GAL NAG GAL BGC n/a n/a
25 4MBY - SIA GAL n/a n/a
26 4MBZ - SIA GAL n/a n/a
27 4FMI - NAG SIA GAL n/a n/a
28 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
29 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 35 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; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL 1 1
2 GAL SIA 0.714286 0.960784
3 SIA GAL NAG GAL 0.693878 0.943396
4 SIA 2FG 0.689655 0.890909
5 NAG SIA GAL 0.632653 0.924528
6 GAL NGA GAL SIA 0.631068 0.943396
7 SIA GAL NAG 0.63 0.909091
8 NGA GAL SIA 0.622449 0.924528
9 SIA GAL A2G 0.622449 0.924528
10 BGC SIA GAL 0.616162 0.960784
11 SIA GAL GLC 0.616162 0.960784
12 GAL BGC SIA 0.616162 0.960784
13 BGC GAL SIA 0.616162 0.960784
14 GLA GLC SIA 0.616162 0.960784
15 SIA GAL BGC 0.616162 0.960784
16 SIA 2FG NAG 0.613861 0.859649
17 SIA SIA GAL 0.612245 0.907407
18 SIA GAL NDG SIA 0.59434 0.909091
19 SIA GAL NGA 0.594059 0.924528
20 NGC MBG 0.585106 0.90566
21 NAG GAL NGC 0.575472 0.924528
22 SIA GAL NGS 0.574074 0.731343
23 SIA GAL NGA GAL 0.570093 0.924528
24 GAL SIA NGA GAL 0.570093 0.924528
25 GAL SIA NGA GAL SIA 0.570093 0.924528
26 SIA GAL NAG SIA 0.564815 0.943396
27 SIA GLA NAG FUC 0.54955 0.924528
28 SIA GAL NAG FUC 0.54955 0.924528
29 FUC NDG GAL SIA 0.54955 0.924528
30 NAG FUC SIA GAL 0.54955 0.924528
31 SIA GAL NDG FUC 0.54955 0.924528
32 NDG FUC SIA GAL 0.54955 0.924528
33 BGC SIA SIA GAL 0.539823 0.907407
34 SIA SIA GLA BGC 0.539823 0.907407
35 SIA NAG GAL 0.537736 0.909091
36 SIA GAL MAG FUC 0.535714 0.888889
37 SIA NAG 0.53125 0.909091
38 SIA GAL BGC NGA 0.530973 0.924528
39 GAL BGC SIA NGA 0.530973 0.924528
40 BGC GAL SIA NGA 0.530973 0.924528
41 BGC GAL SIA SIA GAL NGA 0.525862 0.924528
42 BGC GAL SIA NGA GAL SIA 0.525862 0.924528
43 MNA 0.52439 0.849057
44 GAL NGA GAL BGC SIA 0.521368 0.924528
45 SIA GAL BGC NGA GAL 0.521368 0.924528
46 BGC GAL SIA NGA GAL 0.521368 0.924528
47 GAL NGA SIA GAL BGC 0.521368 0.924528
48 4U2 0.519231 0.90566
49 NAG GAL SIA 0.514019 0.943396
50 MN0 GAL GLC 0.514019 0.923077
51 GAL TNR SIA 0.508929 0.909091
52 NGC GAL NGA POL AZI 0.508475 0.753846
53 SIA SIA GAL NGA GAL SIA 0.508333 0.907407
54 SLT 0.504762 0.941176
55 SIA SIA GAL NGA GAL 0.504132 0.907407
56 SIA GLA NGS FUC 0.504132 0.731343
57 SIA SIA 0.489583 0.888889
58 SLB SIA 0.489583 0.888889
59 SIA NAG GAL GAL 0.486726 0.943396
60 SLB SIA SIA 0.484536 0.888889
61 SIA SIA SIA SIA SIA SIA SIA 0.484536 0.888889
62 SIA GAL SIA GLC NGA 0.472441 0.907407
63 SIA GAL SIA BGC NGA 0.472441 0.907407
64 GAL NAG SIA GAL 0.470085 0.943396
65 SIA SIA SIA 0.460784 0.888889
66 4U1 0.459459 0.924528
67 4U0 0.45045 0.960784
68 SIA GAL BGC 16C 0.448529 0.806452
69 BGC 18C GAL SIA 0.442029 0.806452
70 SIA WIA 0.441176 0.892857
71 SIA GAL NAG GAL GLC 0.44 0.943396
72 BGC GAL NAG SIA GAL 0.44 0.943396
73 SIA GAL NAG GAL BGC 0.44 0.943396
74 SLB 0.435294 0.86
75 SIA 0.435294 0.86
76 CNP 0.428571 0.796296
77 BGC GAL CEQ SLB NGA GAL SIA SIA 0.425532 0.777778
78 MN0 0.422222 0.849057
79 SIA GAL SIA BGC NGA CEQ 0.41844 0.769231
80 MUS 0.416667 0.793103
81 NXD 0.410526 0.789474
82 SID 0.404255 0.781818
83 BND 0.401961 0.803571
Ligand no: 2; Ligand: BGC SIA GAL; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC SIA GAL 1 1
2 GLA GLC SIA 1 1
3 SIA GAL BGC 1 1
4 SIA GAL GLC 1 1
5 BGC GAL SIA 1 1
6 GAL BGC SIA 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 SIA GAL NGA GAL 0.781818 0.943396
15 SIA GAL A2G 0.765306 0.961538
16 NGA GAL SIA 0.765306 0.961538
17 GAL NGA GAL BGC SIA 0.761468 0.961538
18 SIA GAL BGC NGA GAL 0.761468 0.961538
19 GAL NGA SIA GAL BGC 0.761468 0.961538
20 BGC GAL SIA NGA GAL 0.761468 0.961538
21 NAG GAL NGC 0.757282 0.961538
22 SIA GAL NAG 0.752475 0.909091
23 GAL SIA NGA GAL SIA 0.75 0.961538
24 GAL BGC SIA NGA 0.747664 0.961538
25 BGC GAL SIA NGA 0.747664 0.961538
26 SIA GAL BGC NGA 0.747664 0.961538
27 SIA GAL NGS 0.719626 0.757576
28 GAL SIA 0.717391 1
29 SIA GAL NAG GAL 0.698113 0.943396
30 SIA GAL NAG SIA 0.694444 0.943396
31 SIA GAL NDG FUC 0.690909 0.961538
32 FUC NDG GAL SIA 0.690909 0.961538
33 NDG FUC SIA GAL 0.690909 0.961538
34 NAG FUC SIA GAL 0.690909 0.961538
35 SIA GLA NAG FUC 0.690909 0.961538
36 SIA GAL NAG FUC 0.690909 0.961538
37 4U2 0.686275 0.942308
38 SIA GAL NDG SIA 0.678899 0.909091
39 GAL SIA NGA GAL 0.669725 0.961538
40 SIA GAL NGA GAL 0.669725 0.961538
41 SIA SIA GAL NGA GAL SIA 0.666667 0.943396
42 SIA GAL SIA GLC NGA 0.661157 0.943396
43 SIA GAL SIA BGC NGA 0.661157 0.943396
44 SIA GAL MAG FUC 0.660714 0.924528
45 SIA GAL NAG GAL GLC 0.65812 0.943396
46 SIA GAL NAG GAL BGC 0.65812 0.943396
47 BGC GAL NAG SIA GAL 0.65812 0.943396
48 SIA 2FG 0.642857 0.925926
49 SIA GAL NGA 0.635514 0.961538
50 4U0 0.635514 0.960784
51 SIA SIA GAL 0.622642 0.943396
52 SIA GLA NGS FUC 0.619835 0.757576
53 SIA GAL 0.616162 0.960784
54 NGC MBG 0.613861 0.942308
55 GAL NGA GAL SIA 0.610619 0.943396
56 SIA 2FG NAG 0.609091 0.892857
57 NGC GAL NGA POL AZI 0.6 0.78125
58 SIA GAL BGC 16C 0.598485 0.806452
59 NAG GAL SIA 0.585586 0.943396
60 BGC 18C GAL SIA 0.577778 0.806452
61 BGC GAL CEQ SLB NGA GAL SIA SIA 0.569343 0.806452
62 SIA NAG GAL 0.552632 0.909091
63 GAL NAG SIA GAL 0.55 0.943396
64 SIA NAG GAL GAL 0.542373 0.943396
65 4U1 0.530435 0.924528
66 GAL TNR SIA 0.512397 0.909091
67 SIA GAL SIA BGC NGA CEQ 0.496504 0.769231
68 BGC 18C GAL NGA SIA GAL 0.483871 0.806452
69 NAG GAL BGC 0.466019 0.9
70 LAT NAG GAL 0.462264 0.9
71 GLC GAL NAG GAL 0.462264 0.9
72 GAL NAG GAL GLC 0.457143 0.9
73 BGC GAL NAG GAL 0.457143 0.9
74 MNA 0.447917 0.849057
75 NGA GLA GAL BGC 0.444444 0.9
76 SIA SIA 0.440367 0.924528
77 GAL NGA GLA BGC GAL 0.440367 0.9
78 SLB SIA 0.440367 0.924528
79 SIA NAG 0.4375 0.875
80 SIA SIA SIA SIA SIA SIA SIA 0.436364 0.924528
81 SLB SIA SIA 0.436364 0.924528
82 SIA SIA SIA 0.429825 0.924528
83 NGA GAL BGC 0.413462 0.9
84 SIA WIA 0.412281 0.892857
85 FUC GAL NAG GAL BGC 0.40678 0.882353
86 GAL GLC NAG GAL FUC 0.40678 0.882353
87 GLC NAG GAL GAL FUC 0.40678 0.882353
88 GLC GAL NAG GAL FUC FUC 0.404959 0.901961
89 BGC GAL NAG GAL FUC FUC 0.404959 0.901961
90 MUS 0.403361 0.793103
91 GLA GAL GAL 0.402062 0.66
92 SLB 0.402062 0.86
93 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: 61
This union binding pocket(no: 1) in the query (biounit: 4mby.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2GC0 PAN 1.06383
2 5C9P FUC 1.07914
3 6GNO XDI 1.48148
4 5N9T 8QQ 1.79856
5 2Y91 98J 1.79856
6 3I8P 840 2.15827
7 5WBF LAC 2.22222
8 2IFB PLM 2.29008
9 3R7F CP 2.51799
10 5BUK FAD 2.51799
11 4CYI ATP 2.51799
12 3MQG ACO 2.60417
13 1KJ1 MAN 2.75229
14 4O9S 2RY 2.7907
15 1GA8 DEL 2.8777
16 1GA8 UPF 2.8777
17 3TCT 3MI 3.14961
18 1QXO FMN 3.23741
19 5THQ NDP 3.67647
20 5TZO 7V7 3.7234
21 3U2U UDP 3.80228
22 3LXK MI1 3.95683
23 2NVA PL2 3.95683
24 1SU2 ATP 4.40252
25 5BW4 SAM 4.67626
26 1DTD GLU 4.67626
27 3ZL8 ADP 4.67626
28 3EEB IHP 4.78469
29 1I1N SAH 4.86726
30 5DEX 5E0 5.03597
31 1UNQ 4IP 5.6
32 3V91 UPG 5.7554
33 1V8B NAD 5.7554
34 3SWC SAH 5.7554
35 3ZOD HQE 5.75916
36 3ZOD FMN 5.75916
37 1EC9 XYH 6.11511
38 3LL5 ADP 6.4257
39 3LL5 IPE 6.4257
40 3FN0 TRP ASN TRP PHE ASP ILE THR ASN LYS 6.49351
41 4IPH 1FJ 6.50407
42 5A5W GUO 7.11462
43 4ZOH FAD 7.19424
44 5LWY OLB 7.47664
45 1UW1 ADP 7.5
46 2QO4 CHD 7.93651
47 4M1U A2G MBG 8.57143
48 4M1U MBG A2G 8.57143
49 1LR8 IHS 9.45946
50 3CU0 GAL GAL SO4 9.71223
51 3CU0 UDP 9.71223
52 3UKR CKH 10.0719
53 1QD0 RR6 10.1562
54 3BJK CIT 10.4575
55 3F5K CE5 10.7914
56 4YEF 4CQ 11.236
57 2BOS GLA GAL 13.2353
58 3E8N VRA 14.0288
59 3E8N ATP 14.0288
60 5Z84 PEK 25.4237
61 4NG2 OHN 25.6637
Pocket No.: 2; Query (leader) PDB : 4MBY; Ligand: BGC SIA GAL; Similar sites found with APoc: 23
This union binding pocket(no: 2) in the query (biounit: 4mby.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1ID0 ANP None
2 1VFS DCS 1.79856
3 1XRO LEU 2.51799
4 3VC3 C6P 2.51799
5 5O1I 9GH 3.19635
6 3UDG TMP 3.23741
7 6F6J SIN 3.23741
8 2GJN NIS 3.59712
9 2QE0 NAP 3.59712
10 1D6S PLP MET 3.59712
11 6ECT SAM 3.95683
12 1I7E IBS 4.15094
13 1Z0N BCD 4.16667
14 4QNW FMN 5.39568
15 3GE7 AFQ 5.7554
16 3WQD PLP 999 6.11511
17 2FLI DX5 7.27273
18 1EFV AMP 7.91367
19 1EFV FAD 7.91367
20 1GPE FAD 7.91367
21 5J6A P46 8.63309
22 2WOX NDP 11.1511
23 2BOS GLA GAL GLC 13.2353
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