Receptor
PDB id Resolution Class Description Source Keywords
4POT 2.1 Å NON-ENZYME: OTHER STRUCTURE OF HUMAN POLYOMAVIRUS 9 VP1 PENTAMER IN COMPLEX WI GLYCOLYLNEURAMINIC ACID CONTAINING 3'-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
NAG GAL NGC E:405;
B:405;
H:405;
D:407;
I:405;
C:407;
A:405;
J:406;
F:406;
G:408;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
689.597 n/a O=C([...
EDO D:402;
A:402;
G:403;
F:404;
A:403;
J:402;
D:405;
G:406;
B:403;
E:403;
H:402;
E:402;
C:405;
G:404;
B:402;
G:405;
I:403;
I:402;
J:403;
F:402;
G:402;
C:403;
H:403;
J:404;
D:403;
D:404;
C:402;
F:403;
C: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;
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 I:404;
G:407;
D:406;
H:404;
J:405;
C:406;
F:405;
B:404;
E:404;
A:404;
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 1256 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 (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: NAG GAL NGC; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL NGC 1 1
2 NAG SIA GAL 0.905263 0.962264
3 SIA GAL NAG 0.905263 0.962264
4 MN0 GAL GLC 0.794118 0.961538
5 SIA GAL NGS 0.768519 0.784615
6 GAL BGC SIA 0.757282 0.961538
7 SIA BGC GAL 0.757282 0.961538
8 SIA GAL BGC 0.757282 0.961538
9 BGC GAL SIA 0.757282 0.961538
10 SIA GAL GLC 0.757282 0.961538
11 BGC SIA GAL 0.757282 0.961538
12 GLA GLC SIA 0.757282 0.961538
13 4U2 0.754902 0.943396
14 NGA GAL SIA 0.714286 0.962264
15 SIA GAL A2G 0.714286 0.962264
16 NGC MBG 0.7 0.943396
17 SIA GAL NGA GAL 0.6875 0.962264
18 GAL NGA GAL SIA 0.6875 0.962264
19 NGC GAL NGA POL AZI 0.686441 0.8125
20 BGC SIA SIA GAL 0.666667 0.944444
21 SIA SIA GLA BGC 0.666667 0.944444
22 SIA GLA NAG FUC 0.663793 0.962264
23 SIA GAL NDG FUC 0.663793 0.962264
24 NAG FUC SIA GAL 0.663793 0.962264
25 NDG FUC SIA GAL 0.663793 0.962264
26 FUC NDG GAL SIA 0.663793 0.962264
27 SIA GAL NAG FUC 0.663793 0.962264
28 GAL SIA NGA GAL SIA 0.657895 0.962264
29 SIA GAL NAG SIA 0.652174 0.944444
30 BGC GAL SIA SIA GAL NGA 0.65 0.962264
31 GAL BGC GAL SIA NGA SIA 0.65 0.962264
32 NAG GAL SIA 0.633929 0.944444
33 SIA GAL 0.633663 0.961538
34 SLT 0.627273 0.942308
35 SIA GAL NDG SIA 0.623932 0.945455
36 SIA SIA GAL NGA GAL 0.611111 0.944444
37 SIA GAL MAG FUC 0.608333 0.925926
38 GAL BGC SIA NGA 0.603306 0.962264
39 BGC GAL SIA NGA 0.603306 0.962264
40 SIA GAL BGC NGA 0.603306 0.962264
41 SIA GLA NGS FUC 0.598425 0.784615
42 GAL NGA GAL BGC SIA 0.592 0.962264
43 BGC GAL SIA NGA GAL 0.592 0.962264
44 SIA GAL BGC NGA GAL 0.592 0.962264
45 GAL NGA SIA GAL BGC 0.592 0.962264
46 SIA SIA GAL NGA GAL SIA 0.590551 0.944444
47 BGC GAL SIA NGA GAL SIA 0.585185 0.822581
48 SIA 2FG 0.584906 0.892857
49 SIA GAL NGA 0.582609 0.962264
50 4U1 0.577586 0.925926
51 GAL SIA NGA GAL 0.575 0.962264
52 SIA 2FG NAG 0.57265 0.894737
53 SIA GAL NAG GAL GLC 0.55814 0.944444
54 BGC GAL NAG SIA GAL 0.55814 0.944444
55 SIA GAL NAG GAL BGC 0.55814 0.944444
56 SIA GAL BGC 16C 0.557143 0.83871
57 SIA SIA GAL 0.556522 0.944444
58 5N6 GAL 0.54955 0.925926
59 SIA GAL SIA BGC NGA 0.540741 0.944444
60 SIA GAL SIA GLC NGA 0.540741 0.944444
61 BGC 18C GAL SIA 0.538462 0.83871
62 GAL NAG SIA GAL 0.531746 0.944444
63 SIA GAL NAG GAL 0.531746 0.944444
64 Z3Q GAL 5N6 0.527132 0.83871
65 BGC GAL CEQ SLB NGA GAL SIA SIA 0.520548 0.836066
66 SIA NAG GAL 0.495935 0.945455
67 4U0 0.479675 0.924528
68 SIA NAG GAL GAL 0.476562 0.944444
69 GAL TNR SIA 0.465116 0.962963
70 NAG GAL NAG 0.462963 0.886792
71 GLA GAL NAG 0.457143 0.865385
72 MAN BMA NAG 0.457143 0.865385
73 NAG GAL GAL 0.457143 0.865385
74 SIA CMO 0.455446 0.836364
75 SIA GAL SIA BGC NGA CEQ 0.453947 0.8
76 GAL SIA 0.451327 0.943396
77 NAG GAL GAL NAG 0.45045 0.886792
78 GAL NAG GAL NAG GAL NAG 0.45045 0.90566
79 MN0 0.446602 0.851852
80 BGC 18C GAL NGA SIA GAL 0.445122 0.83871
81 GAL NDG 0.44 0.865385
82 NLC 0.44 0.865385
83 NDG GAL 0.44 0.865385
84 NAG NDG 0.413462 0.886792
85 CBS 0.413462 0.886792
86 NAG GDL 0.413462 0.886792
87 CBS CBS 0.413462 0.886792
88 G6S NAG 0.405405 0.734375
89 MNA 0.403846 0.818182
90 NAG FUC 0.403846 0.811321
91 SIA SIA 0.401709 0.925926
92 SLB SIA 0.401709 0.925926
93 SIA NAG 0.4 0.910714
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: 14
This union binding pocket(no: 1) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Y88 2ER 0.03636 0.40395 0.819672
2 5A3T MMK 0.01625 0.41644 3.59712
3 4D42 W0I 0.03981 0.41363 3.59712
4 4D42 NAP 0.03981 0.41363 3.59712
5 5BUK FAD 0.02438 0.42124 3.95683
6 2QO4 CHD 0.0289 0.4025 3.96825
7 1V35 NAI 0.01858 0.42491 5.03597
8 1N62 MCN 0.02497 0.41346 5.03597
9 4M1U A2G MBG 0.0001467 0.41854 6.11511
10 5A5W GUO 0.008652 0.44041 9.09091
11 2RGJ FAD 0.03574 0.40228 9.35252
12 1LR8 IHS 0.004336 0.4289 9.45946
13 3FN0 TRP ASN TRP PHE ASP ILE THR ASN LYS 0.004951 0.4321 10.3896
14 5M8T 0TR 0.01541 0.40235 10.7914
Pocket No.: 2; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1XRO LEU 0.02713 0.40955 2.51799
2 1YQS BSA 0.03305 0.40405 2.51799
3 3IES M24 0.04085 0.4003 2.51799
4 4R81 FMN 0.01481 0.40538 3.8835
5 1R27 MGD 0.03176 0.40801 3.95683
6 1MJJ HAL 0.02387 0.40142 6.1674
7 2ZB4 NAP 0.04455 0.40125 7.55396
8 2ZB4 5OP 0.04636 0.40125 7.55396
9 2X32 OTP 0.04762 0.40646 7.82123
Pocket No.: 3; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5JFS 6K0 0.04369 0.40262 2.15827
2 2TPS TPS 0.01772 0.40931 2.20264
3 3KLJ FAD 0.03922 0.40019 3.59712
4 2IV2 MGD 0.04065 0.4024 5.39568
5 4GCZ FMN 0.01084 0.41017 7.91367
Pocket No.: 4; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3AHC TPP 0.03181 0.40156 6.47482
2 4FE2 ASP 0.02206 0.40055 6.66667
Pocket No.: 5; Query (leader) PDB : 4POS; Ligand: NAG SIA GAL; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 4pos.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4Q0L V14 0.02642 0.4006 3.04183
2 1OFD AKG 0.03053 0.40583 6.83453
3 4HP0 NOJ NAG NAG NAG 0.02559 0.40264 8.52713
4 1V8B NAD 0.04296 0.40114 10.7914
Feedback