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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:402;
B:601;
C:402;
D:601;
E:601;
F:601;
G:601;
H:402;
I:601;
J:601;
K:404;
L:401;
M:404;
N:402;
O:403;
P:402;
Q:404;
R:601;
S:403;
T:404;
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:401;
C:401;
K:403;
M:403;
N:401;
P:401;
Q:403;
T:403;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SIA H:401;
Valid;
none;
submit data
309.27 C11 H19 N O9 CC(=O...
SIA GAL M:401;
O:401;
S:401;
K:401;
Q:401;
T:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
454.405 n/a O=C(N...
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 1443 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 (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; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 18D 0.758621 0.955556
4 42D 0.758621 0.875
5 NGC 0.754386 0.933333
6 NGE 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
9 CNP 0.58209 0.875
10 KDN 0.568965 0.72093
11 KDM 0.568965 0.72093
12 SIA SIA 0.565789 0.826923
13 SLB SIA 0.565789 0.826923
14 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 FSI 0.515152 0.895833
17 6KL 0.5 0.807692
18 SFJ 0.5 0.875
19 MN0 0.485714 0.895833
20 EQP 0.470588 0.788462
21 AXP 0.470588 0.788462
22 GAL SIA 0.463415 0.86
23 SID 0.459459 0.82
24 SIA SIA SIA 0.453488 0.826923
25 MUS 0.449438 0.796296
26 NXD 0.447368 0.792453
27 SIA WIA 0.447059 0.767857
28 SIA 2FG 0.447059 0.796296
29 SLT 0.44086 0.877551
30 KDO 0.435484 0.704545
31 SIA GAL 0.435294 0.86
32 SIA NAG 0.430233 0.781818
33 4U0 0.427083 0.86
34 4U2 0.425532 0.843137
35 BND 0.416667 0.807692
36 SKD 0.414286 0.875
37 SIA SIA GAL 0.410526 0.811321
38 4U1 0.408163 0.826923
39 E3M 0.402778 0.606061
40 SIA GAL GLC 0.402062 0.86
41 BGC SIA GAL 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 BGC GAL SIA 0.402062 0.86
44 SIA GAL BGC 0.402062 0.86
45 GLA GLC SIA 0.402062 0.86
46 4AM 0.4 0.833333
47 DAN 0.4 0.911111
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FMJ; Ligand: SIA; Similar sites found with APoc: 13
This union binding pocket(no: 1) in the query (biounit: 4fmj.bio2) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 4C6H HE2 4.49827
2 1JNQ EGT 4.49827
3 5YIC 8VO 4.84429
4 1ZK7 FAD 5.88235
5 4V15 PLP 6.22837
6 4R3L COA 7.51445
7 5LVP ATP 7.61246
8 4TR9 38D 9.34256
9 1W0J ADP 9.55882
10 3ZIA ATP 10.1449
11 3ZIA ADP 10.1449
12 2V7Q ATP 15.0685
13 2CK3 ANP 15.0685
Pocket No.: 2; Query (leader) PDB : 4FMJ; Ligand: 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: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4FMJ; Ligand: SIA GAL; Similar sites found with APoc: 18
This union binding pocket(no: 3) in the query (biounit: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 2IID FAD 2.07612
2 2IID PHE 2.07612
3 5L8L ADP 2.5641
4 4C6H HE2 4.49827
5 1JNQ EGT 4.49827
6 5YIC 8VO 4.84429
7 1KOR ARG 5.19031
8 1KOR ANP 5.19031
9 1KOR SIN 5.19031
10 4V15 PLP 6.22837
11 5LVP ATP 7.61246
12 2OQ2 A3P 8.04598
13 1W0J ADP 9.55882
14 3ZIA ATP 10.1449
15 3ZIA ADP 10.1449
16 4C2W ANP 11.5385
17 4Z87 5GP 12.8028
18 2V7Q ATP 15.0685
Pocket No.: 4; Query (leader) PDB : 4FMJ; Ligand: SIA GAL; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 4fmj.bio6) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 1SR7 MOF 4.2471
2 1SL6 GAL NDG FUC 19.0217
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