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Receptor
PDB id Resolution Class Description Source Keywords
3BWR 2.25 Å NON-ENZYME: OTHER SV40 VP1 PENTAMER IN COMPLEX WITH GM1 OLIGOSACCHARIDE SIMIAN VIRUS 40 SV40 GM1 VIRAL RECEPTOR VIRAL ATTACHMENT GANGLIOSIDE VPPOLYOMAVIRUSES CAPSID PROTEIN LATE PROTEIN NUCLEUS VIRIPROTEIN
Ref.: STRUCTURAL BASIS OF GM1 GANGLIOSIDE RECOGNITION BY VIRUS 40. PROC.NATL.ACAD.SCI.USA V. 105 5219 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:3;
A:9;
B:1;
C:2;
D:4;
E:5;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GAL NGA SIA GAL BGC A:299;
C:299;
E:299;
Valid;
Valid;
Valid;
none;
none;
none;
Kd ~ 3 mM
997.88 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BWR 2.25 Å NON-ENZYME: OTHER SV40 VP1 PENTAMER IN COMPLEX WITH GM1 OLIGOSACCHARIDE SIMIAN VIRUS 40 SV40 GM1 VIRAL RECEPTOR VIRAL ATTACHMENT GANGLIOSIDE VPPOLYOMAVIRUSES CAPSID PROTEIN LATE PROTEIN NUCLEUS VIRIPROTEIN
Ref.: STRUCTURAL BASIS OF GM1 GANGLIOSIDE RECOGNITION BY VIRUS 40. PROC.NATL.ACAD.SCI.USA V. 105 5219 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC 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: GAL NGA SIA GAL BGC; Similar ligands found: 86
No: Ligand ECFP6 Tc MDL keys Tc
1 GAL NGA SIA GAL BGC 1 1
2 BGC GAL SIA NGA GAL 1 1
3 GAL NGA GAL BGC SIA 1 1
4 SIA GAL BGC NGA GAL 1 1
5 BGC GAL SIA SIA GAL NGA 0.917431 1
6 BGC GAL SIA NGA GAL SIA 0.917431 1
7 SIA GAL NGA GAL 0.834862 1
8 GAL SIA NGA GAL 0.834862 1
9 SIA GAL BGC NGA 0.830357 1
10 BGC GAL SIA NGA 0.830357 1
11 GAL BGC SIA NGA 0.830357 1
12 GAL SIA NGA GAL SIA 0.769912 1
13 SIA GAL GLC 0.761468 0.961538
14 GAL BGC SIA 0.761468 0.961538
15 GLA GLC SIA 0.761468 0.961538
16 BGC SIA GAL 0.761468 0.961538
17 BGC GAL SIA 0.761468 0.961538
18 SIA GAL BGC 0.761468 0.961538
19 SIA GAL SIA BGC NGA 0.738095 0.981132
20 SIA GAL SIA GLC NGA 0.738095 0.981132
21 SIA SIA GAL NGA GAL 0.725806 0.981132
22 GAL NGA GAL SIA 0.724138 0.981132
23 SIA SIA GAL NGA GAL SIA 0.690476 0.981132
24 SIA SIA GLA BGC 0.674797 0.981132
25 BGC SIA SIA GAL 0.674797 0.981132
26 SIA GAL NGA 0.663793 1
27 MN0 GAL GLC 0.65812 0.924528
28 BGC GAL CEQ SLB NGA GAL SIA SIA 0.652482 0.83871
29 SLT 0.652174 0.942308
30 SIA GAL NAG GAL 0.65 0.981132
31 BGC 18C GAL NGA SIA GAL 0.642384 0.83871
32 NAG SIA GAL 0.641026 1
33 SIA GAL A2G 0.632479 1
34 NGA GAL SIA 0.632479 1
35 BGC GAL NAG SIA GAL 0.630769 0.981132
36 SIA GAL NAG GAL BGC 0.630769 0.981132
37 SIA GAL NAG GAL GLC 0.630769 0.981132
38 SIA NAG GAL GAL 0.6 0.981132
39 SIA GAL NAG 0.598361 0.945455
40 4U0 0.595041 0.924528
41 NAG GAL NGC 0.592 0.962264
42 SIA GAL NAG SIA 0.582677 0.981132
43 SIA GAL MAG FUC 0.581395 0.962264
44 SIA GAL NDG FUC 0.581395 1
45 FUC NDG GAL SIA 0.581395 1
46 NDG FUC SIA GAL 0.581395 1
47 NAG FUC SIA GAL 0.581395 1
48 SIA GAL NAG FUC 0.581395 1
49 SIA GLA NAG FUC 0.581395 1
50 SIA GAL NGS 0.578125 0.787879
51 SIA GAL NDG SIA 0.55814 0.945455
52 GAL SIA 0.557522 0.961538
53 BGC GAL NAG GAL 0.554545 0.865385
54 GAL NAG GAL GLC 0.554545 0.865385
55 NAG GAL SIA 0.552 0.981132
56 GAL NGA GLA BGC GAL 0.548673 0.865385
57 SIA 2FG NAG 0.547619 0.928571
58 SIA NAG GAL 0.547619 0.945455
59 GAL TNR SIA 0.546154 0.945455
60 4U2 0.544715 0.980769
61 GAL NAG SIA GAL 0.533835 0.981132
62 NGC GAL NGA POL AZI 0.532847 0.784615
63 SIA 2FG 0.529915 0.892857
64 SIA GLA NGS FUC 0.528571 0.787879
65 SIA GAL SIA BGC NGA CEQ 0.526316 0.8
66 SIA GAL 0.521368 0.924528
67 SIA GAL BGC 16C 0.506579 0.83871
68 4U1 0.503876 0.962264
69 SIA SIA GAL 0.496063 0.981132
70 BGC 18C GAL SIA 0.490323 0.83871
71 NGC MBG 0.483607 0.907407
72 GAL GLC NAG GAL FUC 0.472 0.884615
73 GLC NAG GAL GAL FUC 0.472 0.884615
74 FUC GAL NAG GAL BGC 0.472 0.884615
75 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.466667 0.962963
76 GLC GAL NAG GAL 0.466102 0.865385
77 LAT NAG GAL 0.466102 0.865385
78 GLA GAL NAG FUC GAL GLC 0.465116 0.884615
79 NGA GLA GAL BGC 0.45 0.865385
80 BGC GAL NAG GAL FUC FUC 0.446154 0.903846
81 GLC GAL NAG GAL FUC FUC 0.446154 0.903846
82 NAG GAL BGC 0.444444 0.865385
83 GLC GAL NAG GAL FUC A2G 0.426471 0.942308
84 A2G GAL NAG FUC GAL GLC 0.426471 0.942308
85 NGA GAL BGC 0.422414 0.865385
86 GLA GAL GAL 0.4 0.634615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BWR; Ligand: GAL NGA SIA GAL BGC; Similar sites found with APoc: 28
This union binding pocket(no: 1) in the query (biounit: 3bwr.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 5OO5 UUA None
2 1DZK PRZ 1.91083
3 3I59 N6S 2.00803
4 3I59 N6R 2.00803
5 5XDT MB3 2.92208
6 1S4M LUM 2.94118
7 1NB9 ADP 3.40136
8 1NB9 RBF 3.40136
9 6BYM HC3 3.44828
10 1R27 MGD 3.67647
11 3PE2 E1B 4.41176
12 1XOC VAL ASP SER LYS ASN THR SER SER TRP 4.41176
13 4EUO ABU 4.41176
14 2HRL SIA GAL SIA BGC NGA CEQ 4.72441
15 4LAE 1VM 4.79042
16 4LAE NAP 4.79042
17 1M5B BN1 5.32319
18 6CAY ERG 5.32544
19 4M1U MBG A2G 7.14286
20 1N07 FMN 7.36196
21 1SQL GUN 7.53425
22 5A89 ADP 8.33333
23 5A89 FMN 8.33333
24 1GPM AMP 8.82353
25 3UG4 AHR 9.55882
26 2BOS GLA GAL GLC 19.1176
27 2BOS GLA GAL 19.1176
28 4IPH 1FJ 24.3902
Pocket No.: 2; Query (leader) PDB : 3BWR; Ligand: GAL NGA SIA GAL BGC; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 3bwr.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2GU8 796 2.57353
2 3E8N ATP 3.51906
3 3E8N VRA 3.51906
4 1U7Z PMT 3.53982
5 1CX4 CMP 4.77941
6 1SL6 GAL NDG FUC 13.587
7 4WG0 CHD 26.6667
Pocket No.: 3; Query (leader) PDB : 3BWR; Ligand: GAL NGA SIA GAL BGC; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 3bwr.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1SS4 GSH 3.26797
2 2GCG NDP 3.67647
3 4O0L NDP 4.04412
4 4WNB 4BN 5.34759
5 4RUS NDG 6.72269
6 1IOW PHY 7.35294
7 1KBI PYR 9.55882
8 1KBI FMN 9.55882
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