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([...
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 1256 families.
1 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3BWR Kd ~ 3 mM GAL NGA SIA GAL BGC n/a n/a
2 4X17 - SIA SIA 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: GAL NGA SIA GAL BGC; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL SIA NGA GAL 1 1
2 SIA GAL BGC NGA GAL 1 1
3 GAL NGA SIA GAL BGC 1 1
4 GAL NGA GAL BGC SIA 1 1
5 BGC GAL SIA SIA GAL NGA 0.917431 1
6 GAL BGC GAL SIA NGA SIA 0.917431 1
7 GAL SIA NGA GAL 0.834862 1
8 GAL BGC SIA NGA 0.830357 1
9 BGC GAL SIA NGA 0.830357 1
10 SIA GAL BGC NGA 0.830357 1
11 SIA GAL NGA GAL 0.818182 1
12 GAL NGA GAL SIA 0.818182 1
13 GAL SIA NGA GAL SIA 0.769912 1
14 GAL BGC SIA 0.761468 0.961538
15 SIA GAL GLC 0.761468 0.961538
16 BGC SIA GAL 0.761468 0.961538
17 SIA BGC GAL 0.761468 0.961538
18 BGC GAL SIA 0.761468 0.961538
19 GLA GLC SIA 0.761468 0.961538
20 SIA GAL BGC 0.761468 0.961538
21 SIA GAL SIA BGC NGA 0.738095 0.981132
22 SIA GAL SIA GLC NGA 0.738095 0.981132
23 SIA SIA GAL NGA GAL 0.725806 0.981132
24 BGC GAL SIA NGA GAL SIA 0.704545 0.852459
25 SIA SIA GAL NGA GAL SIA 0.690476 0.981132
26 SIA SIA GLA BGC 0.674797 0.981132
27 BGC SIA SIA GAL 0.674797 0.981132
28 BGC GAL CEQ SLB NGA GAL SIA SIA 0.664286 0.866667
29 SIA GAL NGA 0.663793 1
30 MN0 GAL GLC 0.65812 0.924528
31 SLT 0.652174 0.942308
32 BGC 18C GAL NGA SIA GAL 0.642384 0.83871
33 SIA GAL NAG 0.641026 1
34 NAG SIA GAL 0.641026 1
35 NGA GAL SIA 0.632479 1
36 SIA GAL A2G 0.632479 1
37 BGC GAL NAG SIA GAL 0.630769 0.981132
38 SIA GAL NAG GAL GLC 0.630769 0.981132
39 SIA GAL NAG GAL BGC 0.630769 0.981132
40 SIA NAG GAL GAL 0.6 0.981132
41 4U0 0.595041 0.924528
42 NAG GAL NGC 0.592 0.962264
43 SIA GAL NGS 0.590551 0.8125
44 SIA GAL NAG SIA 0.582677 0.981132
45 SIA GAL NAG FUC 0.581395 1
46 SIA GLA NAG FUC 0.581395 1
47 NAG FUC SIA GAL 0.581395 1
48 SIA GAL NDG FUC 0.581395 1
49 SIA GAL MAG FUC 0.581395 0.962264
50 NDG FUC SIA GAL 0.581395 1
51 FUC NDG GAL SIA 0.581395 1
52 SIA GAL NDG SIA 0.55814 0.945455
53 SIA GAL 0.557522 0.961538
54 BGC GAL NAG GAL 0.554545 0.865385
55 GAL NAG GAL BGC 0.554545 0.865385
56 LAT NAG GAL 0.554545 0.865385
57 NAG GAL SIA 0.552 0.981132
58 GAL TNR SIA 0.550388 0.962963
59 GAL NGA GLA BGC GAL 0.548673 0.865385
60 SIA NAG GAL 0.547619 0.945455
61 SIA 2FG NAG 0.547619 0.928571
62 4U2 0.544715 0.980769
63 SIA GLA NGS FUC 0.539568 0.8125
64 GAL NAG SIA GAL 0.533835 0.981132
65 SIA GAL NAG GAL 0.533835 0.981132
66 NGC GAL NGA POL AZI 0.532847 0.784615
67 SIA 2FG 0.529915 0.892857
68 SIA GAL SIA BGC NGA CEQ 0.526316 0.8
69 Z3Q GAL 5N6 0.518248 0.83871
70 SIA GAL BGC 16C 0.506579 0.83871
71 4U1 0.503876 0.962264
72 5N6 GAL 0.5 0.962264
73 SIA SIA GAL 0.496063 0.981132
74 BGC 18C GAL SIA 0.490323 0.83871
75 NGC MBG 0.483607 0.907407
76 GAL SIA 0.483051 0.943396
77 FUC GAL NAG GAL BGC 0.472 0.884615
78 6PZ ACY ACY BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.466667 0.962963
79 ACY ACY 6PZ BGC GAL 1GN ACY 1GN GAL GAL ACY BGC 0.466667 0.962963
80 GLC GAL NAG GAL 0.466102 0.865385
81 GLA GAL NAG FUC GAL GLC 0.465116 0.884615
82 NGA GLA GAL BGC 0.45 0.865385
83 GLC GAL NAG GAL FUC FUC 0.446154 0.903846
84 BGC GAL NAG GAL FUC FUC 0.446154 0.903846
85 NAG GAL BGC 0.444444 0.865385
86 6PZ BGC GAL 1GN 1GN ACY GAL GAL ACY BGC 0.435065 0.962963
87 A2G GAL NAG FUC GAL GLC 0.426471 0.942308
88 GLC GAL NAG GAL FUC A2G 0.426471 0.942308
89 SIA CMO 0.423423 0.87037
90 NGA GAL BGC 0.422414 0.865385
91 GLA GAL BGC 0.4 0.634615
92 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: 19
This union binding pocket(no: 1) in the query (biounit: 3bwr.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5OO5 UUA 0.01754 0.40466 None
2 3I59 N6S 0.004516 0.43849 2.00803
3 3I59 N6R 0.005006 0.43621 2.00803
4 5XDT MB3 0.04457 0.40464 2.92208
5 1S4M LUM 0.02153 0.41459 2.94118
6 1NB9 RBF 0.02476 0.42264 3.40136
7 1NB9 ADP 0.02476 0.42264 3.40136
8 1R2Q GNP 0.03103 0.41322 4.11765
9 4ANW O92 0.04394 0.40283 4.41176
10 2HRL SIA GAL SIA BGC NGA CEQ 0.00727 0.4145 4.72441
11 4LAE NAP 0.04929 0.4158 4.79042
12 4LAE 1VM 0.04929 0.4158 4.79042
13 1M5B BN1 0.009094 0.48211 5.32319
14 4M1U MBG A2G 0.03139 0.40178 7.14286
15 1N07 FMN 0.03404 0.40995 7.36196
16 5A89 ADP 0.03208 0.4201 8.33333
17 5A89 FMN 0.03208 0.4201 8.33333
18 4HP0 NOJ NAG NAG NAG 0.009308 0.43382 14.7287
19 4IPH 1FJ 0.03256 0.40236 24.3902
Pocket No.: 2; Query (leader) PDB : 3BWR; Ligand: GAL NGA SIA GAL BGC; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 3bwr.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GU8 796 0.03867 0.41934 2.57353
2 1U7Z PMT 0.04005 0.40332 3.53982
3 1CX4 CMP 0.01464 0.40614 4.77941
Pocket No.: 3; Query (leader) PDB : 3BWR; Ligand: GAL NGA SIA GAL BGC; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 3bwr.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5BVE 4VG 0.04699 0.41785 2.20588
2 1SS4 GSH 0.002325 0.43892 3.26797
3 1IOW PHY 0.02126 0.4179 7.35294
4 1IOW ADP 0.02126 0.4179 7.35294
5 1KBI PYR 0.02214 0.40974 9.55882
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