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Receptor
PDB id Resolution Class Description Source Keywords
4POR 2.09 Å NON-ENZYME: OTHER STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WI SIALYLLACTOSE HUMAN POLYOMAVIRUS 9 JELLY ROLL FOLD CAPSID FORMATION RECEPTOR INTERACTION CARBOHYDRATE SIALYLOLIGOSACCHARIDE VIRAL COAT PROTEIN VIPROTEIN
Ref.: CRYSTALLOGRAPHIC AND GLYCAN MICROARRAY ANALYSIS OF POLYOMAVIRUS 9 VP1 IDENTIFIES N-GLYCOLYL NEURAMINIC A RECEPTOR CANDIDATE. J.VIROL. V. 88 6100 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:402;
D:402;
G:403;
F:404;
A:403;
J:402;
D:405;
B:403;
E:403;
A:404;
H:404;
H:402;
E:402;
E:405;
C:405;
G:404;
B:402;
G:405;
I:403;
I:402;
B:404;
F:402;
G:402;
H:405;
I:404;
E:404;
C:403;
H:403;
D:403;
D:404;
C:402;
C:404;
F:403;
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;
submit data
62.068 C2 H6 O2 C(CO)...
CA E:401;
D:401;
C:401;
F:401;
G:401;
A:401;
J:401;
I: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...
IPA E:406;
A:405;
D:406;
C:406;
F:405;
B:405;
J:403;
I:405;
H:406;
G:406;
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 J:405;
E:408;
A:407;
D:408;
F:407;
I:407;
G:408;
H:408;
B:407;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
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
4POS 2 Å NON-ENZYME: OTHER STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WI SIALYLLACTOSAMINE HUMAN POLYOMAVIRUS 9 JELLY ROLL FOLD CAPSID FORMATION RECEPTOR INTERACTION CARBOHYDRATE SIALYLOLIGOSACCHARIDE VIRAL COAT PROTEIN VIPROTEIN
Ref.: CRYSTALLOGRAPHIC AND GLYCAN MICROARRAY ANALYSIS OF POLYOMAVIRUS 9 VP1 IDENTIFIES N-GLYCOLYL NEURAMINIC A RECEPTOR CANDIDATE. J.VIROL. V. 88 6100 2014
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4POR - BGC SIA GAL n/a n/a
2 4POS - NAG SIA GAL n/a n/a
3 4POT - NAG GAL NGC 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: 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 : 4POS; Ligand: NAG SIA GAL; Similar sites found with APoc: 60
This union binding pocket(no: 1) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2Y88 2ER 0.819672
2 1ADO 13P 1.79856
3 5N9T 8QQ 1.79856
4 5WBF LAC 2.22222
5 3MQG ACO 2.60417
6 6A9F 9BF 2.69058
7 4TR9 ASP TRP ASN 2.8777
8 4D1J DGJ 2.8777
9 2C3W GLC GLC GLC GLC 2.94118
10 3GD4 FAD 3.13112
11 5VGS 9A7 3.18471
12 2CDU FAD 3.23741
13 5A3T MMK 3.59712
14 2F2H XTG 3.59712
15 4D42 NAP 3.59712
16 3R7F CP 3.59712
17 4D42 W0I 3.59712
18 1QXO FMN 3.59712
19 2YVJ FAD 3.66972
20 4R81 FMN 3.8835
21 5BUK FAD 3.95683
22 1R27 MGD 3.95683
23 2QO4 CHD 3.96825
24 4R38 RBF 4.28571
25 5BVA FAD 4.31655
26 5I7S E9P 4.34783
27 5I7S NAD 4.34783
28 3E8N ATP 4.39883
29 3E8N VRA 4.39883
30 2BOS GLA GAL GLC 4.41176
31 2BOS GLA GAL 4.41176
32 3BJK CIT 4.57516
33 4A59 AMP 4.67626
34 1V35 NAI 5.03597
35 1N62 MCN 5.03597
36 5M60 BGC 5.03597
37 2GJN NIS 5.7554
38 1EC9 XYH 5.7554
39 1NNU TCT 6.11354
40 1NNU NAD 6.11354
41 4M1U A2G MBG 6.11511
42 4MOB ADP 6.83453
43 1UW1 ADP 7.5
44 3UDG TMP 7.55396
45 5LWY OLB 7.56302
46 5C9P FUC 7.91367
47 2Z6C FMN 8.52713
48 1EU1 MGD 8.63309
49 5NLD LBT 8.63309
50 5A5W GUO 9.09091
51 2RGJ FAD 9.35252
52 1LR8 IHS 9.45946
53 1FFU CDP 9.71223
54 3FN0 TRP ASN TRP PHE ASP ILE THR ASN LYS 10.3896
55 4IPH 1FJ 10.5691
56 1GPE FAD 10.7914
57 5M8T 0TR 10.7914
58 2NPX FAD 16.9065
59 3GE7 AFQ 19.4245
60 5JWP AKG 36.8421
Pocket No.: 2; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found with APoc: 18
This union binding pocket(no: 2) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 6GNO XDI 1.48148
2 5GLT BGC GAL NAG GAL 2.15827
3 1XRO LEU 2.51799
4 1YQS BSA 2.51799
5 3IES M24 2.51799
6 5TZJ UD1 3.23741
7 5V6F MAN BMA MAN 3.62319
8 5VN0 FAD 3.95683
9 2BZ1 TAU 4.59184
10 3NV3 GAL NAG MAN 5.07246
11 4YEF 4CQ 5.61798
12 1MJJ HAL 6.1674
13 2ZB4 NAP 7.55396
14 2ZB4 5OP 7.55396
15 2X32 OTP 7.82123
16 3SLS ANP 8.27338
17 2D6M LBT 10.0629
18 1SWG BTN 13.2812
Pocket No.: 3; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found with APoc: 7
This union binding pocket(no: 3) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2TPS TPS 2.20264
2 3KLJ FAD 3.59712
3 1JG3 ADN 4.68085
4 2IV2 MGD 5.39568
5 5ODQ 9SB 7.14286
6 4GCZ FMN 7.91367
7 2E7Z MGD 13.6691
Pocket No.: 4; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found with APoc: 8
This union binding pocket(no: 4) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4WW8 VD9 3.04183
2 3VZS NAP 3.50195
3 1OX5 1PR 4.31655
4 1KKR 2AS 5.03597
5 1OFD AKG 6.83453
6 1DTD GLU 10.0719
7 1V8B NAD 10.7914
8 2AL2 2PG 15.4676
Pocket No.: 5; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found with APoc: 4
This union binding pocket(no: 5) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3E1T FAD 1.79856
2 3AHC TPP 6.47482
3 4FE2 ASP 6.66667
4 5HCY 60D 9.71223
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