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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO D:402;
A:402;
G:403;
F:404;
B:405;
A:403;
J:402;
B:403;
E:403;
A:404;
H:404;
H:402;
E:402;
B:402;
I:403;
I:402;
B:404;
F:405;
F:402;
A:405;
G:402;
H:405;
I:404;
A:407;
H:403;
A:406;
I:405;
D:403;
C:402;
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;
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...
NAG SIA GAL F:408;
D:406;
E:406;
B:408;
J:405;
G:406;
H:408;
A:410;
I:408;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
673.598 n/a O=C(N...
IPA I:406;
G:404;
C:403;
J:403;
F:406;
E:404;
A:408;
H:406;
D:404;
B: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)...
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: NAG SIA GAL; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG SIA GAL 1 1
2 NAG GAL NGC 0.905263 0.962264
3 GAL BGC SIA 0.831579 0.961538
4 BGC GAL SIA 0.831579 0.961538
5 BGC SIA GAL 0.831579 0.961538
6 SIA GAL GLC 0.831579 0.961538
7 GLA GLC SIA 0.831579 0.961538
8 SIA GAL BGC 0.831579 0.961538
9 4U2 0.829787 0.980769
10 SIA GAL NGS 0.821782 0.787879
11 SIA GAL A2G 0.783505 1
12 NGA GAL SIA 0.783505 1
13 SIA GAL NAG 0.752475 0.945455
14 SIA SIA GLA BGC 0.724771 0.981132
15 BGC SIA SIA GAL 0.724771 0.981132
16 NAG FUC SIA GAL 0.722222 1
17 SIA GLA NAG FUC 0.722222 1
18 SIA GAL NDG FUC 0.722222 1
19 NDG FUC SIA GAL 0.722222 1
20 FUC NDG GAL SIA 0.722222 1
21 SIA GAL NAG FUC 0.722222 1
22 GAL SIA NGA GAL SIA 0.716981 1
23 SIA GAL NAG SIA 0.71028 0.981132
24 MN0 GAL GLC 0.708738 0.924528
25 BGC GAL SIA NGA GAL SIA 0.705357 1
26 BGC GAL SIA SIA GAL NGA 0.705357 1
27 GAL SIA 0.698925 0.961538
28 SIA GAL NAG GAL 0.698113 0.981132
29 NAG GAL SIA 0.692308 0.981132
30 SLT 0.686275 0.942308
31 SIA GAL NDG SIA 0.678899 0.945455
32 SIA SIA GAL NGA GAL 0.661017 0.981132
33 SIA GAL MAG FUC 0.660714 0.962264
34 SIA 2FG 0.642857 0.892857
35 SIA GAL BGC NGA GAL 0.641026 1
36 GAL NGA SIA GAL BGC 0.641026 1
37 BGC GAL SIA NGA GAL 0.641026 1
38 GAL NGA GAL BGC SIA 0.641026 1
39 SIA SIA GAL NGA GAL SIA 0.638655 0.981132
40 SIA GLA NGS FUC 0.633333 0.787879
41 SIA GAL 0.632653 0.924528
42 4U1 0.62963 0.962264
43 GAL BGC SIA NGA 0.626087 1
44 SIA GAL BGC NGA 0.626087 1
45 BGC GAL SIA NGA 0.626087 1
46 SIA GAL NGA GAL 0.625 1
47 GAL SIA NGA GAL 0.625 1
48 SIA 2FG NAG 0.623853 0.928571
49 NGC MBG 0.613861 0.907407
50 NGC GAL NGA POL AZI 0.613445 0.784615
51 SIA SIA GAL 0.607477 0.981132
52 SIA GAL NGA 0.605505 1
53 GAL NGA GAL SIA 0.596491 0.981132
54 SIA GAL BGC 16C 0.586466 0.83871
55 SIA GAL NAG GAL BGC 0.577236 0.981132
56 BGC GAL NAG SIA GAL 0.577236 0.981132
57 SIA GAL NAG GAL GLC 0.577236 0.981132
58 BGC 18C GAL SIA 0.566176 0.83871
59 SIA GAL SIA GLC NGA 0.55814 0.981132
60 SIA GAL SIA BGC NGA 0.55814 0.981132
61 GAL NAG SIA GAL 0.55 0.981132
62 BGC GAL CEQ SLB NGA GAL SIA SIA 0.546763 0.83871
63 SIA NAG GAL 0.53913 0.945455
64 4U0 0.521739 0.924528
65 SIA NAG GAL GAL 0.516667 0.981132
66 GAL TNR SIA 0.5 0.945455
67 MAN BMA NAG 0.489796 0.865385
68 GLA GAL NAG 0.489796 0.865385
69 SIA GAL SIA BGC NGA CEQ 0.486111 0.8
70 GAL NDG 0.473118 0.865385
71 NDG GAL 0.473118 0.865385
72 NLC 0.473118 0.865385
73 NAG GAL GAL NAG 0.466667 0.923077
74 GAL NAG GAL NAG GAL NAG 0.466667 0.942308
75 NAG GAL NAG 0.466019 0.923077
76 BGC 18C GAL NGA SIA GAL 0.464968 0.83871
77 MNA 0.447917 0.851852
78 SLB SIA 0.440367 0.962264
79 SIA SIA 0.440367 0.962264
80 SIA NAG 0.4375 0.910714
81 SIA SIA SIA SIA SIA SIA SIA 0.436364 0.962264
82 SLB SIA SIA 0.436364 0.962264
83 NAG FUC 0.43299 0.846154
84 SIA SIA SIA 0.429825 0.962264
85 G6S NAG 0.419048 0.727273
86 UNU GAL NAG 0.418182 0.90566
87 NAG GDL 0.414141 0.923077
88 NDG NAG 0.414141 0.923077
89 CBS CBS 0.414141 0.923077
90 CBS 0.414141 0.923077
91 SIA WIA 0.412281 0.894737
92 NAG NAG NAG NDG 0.411765 0.942308
93 NAG NAG NAG NAG NAG NAG 0.411765 0.942308
94 NDG NAG NAG NAG 0.411765 0.942308
95 NAG NAG NDG NAG 0.411765 0.942308
96 NAG NAG NAG NAG NDG 0.411765 0.942308
97 NDG NAG NAG 0.411765 0.942308
98 NAG NAG NAG NAG NAG 0.411765 0.942308
99 CTO 0.411765 0.942308
100 NAG NAG NDG 0.411765 0.942308
101 NDG NAG NAG NDG 0.411765 0.942308
102 NAG NAG NAG NAG NAG NAG NAG NAG 0.411765 0.942308
103 TCG 0.407407 0.864407
104 NAG NAG BMA MAN MAN 0.403361 0.923077
105 NAG BMA MAN MAN MAN MAN 0.401709 0.865385
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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