Receptor
PDB id Resolution Class Description Source Keywords
4FMH 1.85 Å NON-ENZYME: OTHER MERKEL CELL POLYOMAVIRUS VP1 IN COMPLEX WITH DISIALYLLACTOSE MERKEL CELL POLYOMAVIRUS VIRAL CAPSID PROTEIN JELLY ROLL ENCAPSIDATION RECEPTOR BISIALYLATED OLIGOSACCHARIDES VIRAL PROTEIN
Ref.: STRUCTURES OF MERKEL CELL POLYOMAVIRUS VP1 COMPLEXE A SIALIC ACID BINDING SITE REQUIRED FOR INFECTION. PLOS PATHOG. V. 8 02738 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:504;
B:405;
C:403;
D:504;
E:404;
F:403;
G:403;
H:405;
I:403;
J:403;
K:405;
L:505;
M:407;
N:404;
O:405;
P:404;
Q:406;
R:505;
S:506;
T:405;
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;
submit data
35.453 Cl [Cl-]
GOL A:501;
A:502;
A:503;
B:403;
B:404;
C:401;
C:402;
D:501;
D:502;
D:503;
E:401;
E:402;
E:403;
F:401;
F:402;
G:401;
G:402;
H:403;
H:404;
I:401;
I:402;
J:401;
J:402;
K:403;
K:404;
K:406;
L:501;
L:502;
L:503;
L:504;
M:403;
M:404;
M:405;
M:406;
N:401;
N:402;
N:403;
O:403;
O:404;
P:401;
P:402;
P:403;
Q:403;
Q:404;
Q:405;
R:501;
R:502;
R:503;
R:504;
S:501;
S:502;
S:503;
S:504;
S:505;
T:403;
T: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;
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;
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
92.094 C3 H8 O3 C(C(C...
SIA GAL B:401;
H:401;
K:401;
M:401;
O:401;
Q:401;
T:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
submit data
470.404 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4FMJ 2.4 Å NON-ENZYME: OTHER MERKEL CELL POLYOMAVIRUS VP1 IN COMPLEX WITH GD1A OLIGOSACCH MERKEL CELL POLYOMAVIRUS VIRAL CAPSID PROTEIN JELLY ROLL ENCAPSIDATION RECEPTOR BISIALYLATED OLIGOSACCHARIDES VIRAL PROTEIN
Ref.: STRUCTURES OF MERKEL CELL POLYOMAVIRUS VP1 COMPLEXE A SIALIC ACID BINDING SITE REQUIRED FOR INFECTION. PLOS PATHOG. V. 8 02738 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4FMI - NAG SIA GAL n/a n/a
2 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
3 4FMH - 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; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL 1 1
2 SIA SIA GAL 0.835294 0.943396
3 5N6 GAL 0.817073 0.961538
4 SIA 2FG 0.790123 0.925926
5 SIA GAL A2G 0.725275 0.961538
6 NGA GAL SIA 0.725275 0.961538
7 BGC SIA GAL 0.717391 1
8 GAL BGC SIA 0.717391 1
9 SIA BGC GAL 0.717391 1
10 SIA GAL GLC 0.717391 1
11 SIA GAL BGC 0.717391 1
12 GLA GLC SIA 0.717391 1
13 BGC GAL SIA 0.717391 1
14 NAG SIA GAL 0.698925 0.961538
15 SIA GAL NAG 0.698925 0.961538
16 GAL SIA NGA GAL SIA 0.676768 0.961538
17 GAL NGA GAL SIA 0.66 0.961538
18 SIA GAL NGA GAL 0.66 0.961538
19 SIA GAL NGA 0.65625 0.961538
20 NGC MBG 0.651685 0.942308
21 SIA 2FG NAG 0.642857 0.892857
22 SIA GAL NAG SIA 0.637255 0.943396
23 NAG GAL NGC 0.633663 0.961538
24 SIA GAL NGS 0.631068 0.78125
25 GAL SIA NGA GAL 0.627451 0.961538
26 SIA SIA GLA BGC 0.622642 0.943396
27 BGC SIA SIA GAL 0.622642 0.943396
28 SIA GAL NDG SIA 0.621359 0.909091
29 FUC NDG GAL SIA 0.619048 0.961538
30 SIA GAL NDG FUC 0.619048 0.961538
31 SIA GLA NAG FUC 0.619048 0.961538
32 NAG FUC SIA GAL 0.619048 0.961538
33 NDG FUC SIA GAL 0.619048 0.961538
34 SIA GAL NAG FUC 0.619048 0.961538
35 SIA CMO 0.61039 0.867925
36 BGC GAL SIA SIA GAL NGA 0.605505 0.961538
37 GAL BGC GAL SIA NGA SIA 0.605505 0.961538
38 GAL SIA 0.602273 0.980392
39 MN0 GAL GLC 0.6 0.960784
40 SIA SIA GAL NGA GAL SIA 0.598214 0.943396
41 SIA GAL MAG FUC 0.588785 0.924528
42 SIA SIA GAL NGA GAL 0.578947 0.943396
43 SLT 0.575758 0.98
44 SIA GAL BGC NGA 0.568807 0.961538
45 GAL BGC SIA NGA 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 0.78125
49 4U2 0.56 0.942308
50 GAL NGA SIA GAL BGC 0.557522 0.961538
51 SIA GAL BGC NGA GAL 0.557522 0.961538
52 BGC GAL SIA NGA GAL 0.557522 0.961538
53 GAL NGA GAL BGC SIA 0.557522 0.961538
54 GAL NAG SIA GAL 0.545455 0.943396
55 SIA GAL NAG GAL 0.545455 0.943396
56 NGC GAL NGA POL AZI 0.54386 0.78125
57 MNA 0.5375 0.849057
58 SIA NAG GAL 0.533333 0.909091
59 BGC GAL SIA NGA GAL SIA 0.528 0.819672
60 NAG GAL SIA 0.52381 0.943396
61 SLB SIA 0.516129 0.924528
62 SIA SIA 0.516129 0.924528
63 Z3Q GAL 5N6 0.513043 0.806452
64 SLB SIA SIA SIA SIA 0.510638 0.924528
65 SIA SIA SIA SLB 0.510638 0.924528
66 SLB SIA SIA 0.510638 0.924528
67 SIA SIA SIA SIA SIA SIA SIA 0.510638 0.924528
68 SIA NAG 0.510417 0.875
69 SIA GAL SIA BGC NGA 0.504065 0.943396
70 SIA GAL SIA GLC NGA 0.504065 0.943396
71 GAL TNR SIA 0.495495 0.925926
72 SIA GAL BGC 16C 0.48855 0.806452
73 4U0 0.485981 0.960784
74 SIA SIA SIA 0.484848 0.924528
75 BGC 18C GAL SIA 0.481203 0.806452
76 BGC GAL CEQ SLB NGA GAL SIA SIA 0.474074 0.833333
77 SIA GAL NAG GAL BGC 0.471074 0.943396
78 BGC GAL NAG SIA GAL 0.471074 0.943396
79 SIA GAL NAG GAL GLC 0.471074 0.943396
80 4U1 0.46789 0.924528
81 SIA 0.463415 0.86
82 SLB 0.463415 0.86
83 SIA WIA 0.45 0.892857
84 CNP 0.438202 0.796296
85 SIA GAL SIA BGC NGA CEQ 0.434783 0.769231
86 MN0 0.431818 0.849057
87 SID 0.413043 0.781818
88 MUS 0.411215 0.793103
89 NXD 0.404255 0.789474
90 C5P SIA 0.403226 0.684932
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FMJ; Ligand: SIA; Similar sites found: 3
This union binding pocket(no: 1) in the query (biounit: 4fmj.bio2) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5LVP ATP 0.01479 0.40113 7.61246
2 1W0J ADP 0.009389 0.43622 9.55882
3 3UR0 SVR 0.01848 0.43486 9.68858
Pocket No.: 2; Query (leader) PDB : 4FMJ; Ligand: SIA; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LYX PGA 0.007737 0.40196 10.0806
2 3ZIA ATP 0.002134 0.4765 10.1449
3 3ZIA ADP 0.004975 0.44908 10.1449
4 2V7Q ATP 0.006862 0.42665 15.0685
Pocket No.: 3; Query (leader) PDB : 4FMJ; Ligand: SIA GAL; Similar sites found: 11
This union binding pocket(no: 3) in the query (biounit: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5L8L ADP 0.01474 0.40067 2.5641
2 1KOR SIN 0.0211 0.43795 5.19031
3 1KOR ANP 0.02141 0.43795 5.19031
4 1KOR ARG 0.0211 0.43795 5.19031
5 5GRF CIT 0.02016 0.40173 7.26644
6 5LVP ATP 0.01269 0.40643 7.61246
7 1W0J ADP 0.01803 0.40743 9.55882
8 3UR0 SVR 0.02 0.43249 9.68858
9 3ZIA ADP 0.005996 0.45115 10.1449
10 3ZIA ATP 0.00389 0.45028 10.1449
11 4C2W ANP 0.01578 0.40003 11.5385
Pocket No.: 4; Query (leader) PDB : 4FMJ; Ligand: SIA GAL; Similar sites found: 3
This union binding pocket(no: 4) in the query (biounit: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SR7 MOF 0.03661 0.40411 4.2471
2 3T2W BTN 0.02235 0.40596 9.01639
3 1SL6 GAL NDG FUC 0.01313 0.40838 19.0217
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