Receptor
PDB id Resolution Class Description Source Keywords
6hkv 1.75 Å NON-ENZYME: STRUCTURAL TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS (TSPYV) VP COMPLEX WITH SIALYLATED PRECISION GLYCOOLIGOMERS TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS SIALIC ACID DERIVATIVE VIRAL PROTEIN
Ref.: DIVALENT SIALYLATED PRECISION GLYCOOLIGOMERS BINDIN POLYOMAVIRUSES AND THE EFFECT OF DIFFERENT LINKERS. MACROMOL BIOSCI V. 19 00426 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL E:402;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
GXB D:401;
J:401;
C:401;
A:401;
I:401;
E:401;
F:401;
G:401;
B:401;
H:401;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.86;
Atoms found LESS than expected: % Diff = 0.753;
Atoms found LESS than expected: % Diff = 0.807;
Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.82;
Atoms found LESS than expected: % Diff = 0.82;
 submit data
2135.19 C92 H139 N19 O39 CC(=O...
MG G:402;
C:402;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
CL C:403;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4U60 1.5 Å NON-ENZYME: STRUCTURAL TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS (TSPYV) VP COMPLEX WITH GM1 OLIGOSACCHARIDE TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS VIRAL COAT PROTEIN JELLY-ROLL FOLD CARBOHYDRATE BINDING VPROTEIN
Ref.: TRICHODYSPLASIA SPINULOSA-ASSOCIATED POLYOMAVIRUS U DISPLACED BINDING SITE ON VP1 TO ENGAGE SIALYLATED GLYCOLIPIDS. PLOS PATHOG. V. 11 05112 2015
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4U60 - BGC GAL SIA NGA GAL n/a n/a
2 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
3 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
4 4U61 - GAL SIA n/a n/a
5 6HKU - GLC GAL SIA n/a n/a
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 44 families.
1 5CPZ - GAL NGA GAL SIA SIA n/a n/a
2 5CPW - GAL SIA NGA GAL SIA SIA n/a n/a
3 5CQ0 - GAL NGA GAL SIA n/a n/a
4 5CPY - GAL NGA GAL SIA n/a n/a
5 1VPS - NAG GAL SIA SIA n/a n/a
6 5CPX - NAG GAL SIA n/a n/a
7 4U60 - BGC GAL SIA NGA GAL n/a n/a
8 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
9 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
10 4U61 - GAL SIA n/a n/a
11 6HKU - GLC GAL SIA n/a n/a
12 4POR - BGC GAL SIA n/a n/a
13 4POS - NAG GAL SIA n/a n/a
14 4POT - NAG GAL NGC n/a n/a
15 4MJ0 - SIA SIA n/a n/a
16 3NXD - BGC GAL NAG GAL SIA n/a n/a
17 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
18 4X15 - BGC GAL SIA NGA n/a n/a
19 4X10 - GAL SIA NGA n/a n/a
20 4X0Z - BGC GAL SIA NGA GAL n/a n/a
21 4X17 - SIA SIA n/a n/a
22 4JCF - NAG GAL SIA n/a n/a
23 4X12 - SIA SIA n/a n/a
24 4X14 - BGC GAL SIA NGA GAL n/a n/a
25 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
26 4X13 - BGC GAL NAG GAL SIA n/a n/a
27 4MBY - GAL SIA n/a n/a
28 4MBZ - GAL SIA n/a n/a
29 4FMI - NAG GAL SIA n/a n/a
30 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
31 4FMH - GAL SIA n/a n/a
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 5CPZ - GAL NGA GAL SIA SIA n/a n/a
2 5CPW - GAL SIA NGA GAL SIA SIA n/a n/a
3 5CQ0 - GAL NGA GAL SIA n/a n/a
4 5CPY - GAL NGA GAL SIA n/a n/a
5 1VPS - NAG GAL SIA SIA n/a n/a
6 5CPX - NAG GAL SIA n/a n/a
7 4U60 - BGC GAL SIA NGA GAL n/a n/a
8 6HKV - GXB C92 H139 N19 O39 CC(=O)NCCN....
9 4U62 - SIA C11 H19 N O9 CC(=O)N[C@....
10 4U61 - GAL SIA n/a n/a
11 6HKU - GLC GAL SIA n/a n/a
12 3BWR Kd ~ 3 mM BGC GAL SIA NGA GAL n/a n/a
13 4POR - BGC GAL SIA n/a n/a
14 4POS - NAG GAL SIA n/a n/a
15 4POT - NAG GAL NGC n/a n/a
16 6Y5Y - BGC GAL SIA n/a n/a
17 4MJ0 - SIA SIA n/a n/a
18 6Y64 - GAL SIA n/a n/a
19 3NXD - BGC GAL NAG GAL SIA n/a n/a
20 4X16 - SIA C11 H19 N O9 CC(=O)N[C@....
21 4X15 - BGC GAL SIA NGA n/a n/a
22 4X10 - GAL SIA NGA n/a n/a
23 4X0Z - BGC GAL SIA NGA GAL n/a n/a
24 4X17 - SIA SIA n/a n/a
25 4JCF - NAG GAL SIA n/a n/a
26 4X12 - SIA SIA n/a n/a
27 4X14 - BGC GAL SIA NGA GAL n/a n/a
28 4X11 - SIA C11 H19 N O9 CC(=O)N[C@....
29 4X13 - BGC GAL NAG GAL SIA n/a n/a
30 4MBY - GAL SIA n/a n/a
31 4MBZ - GAL SIA n/a n/a
32 4FMI - NAG GAL SIA n/a n/a
33 4FMJ - SIA C11 H19 N O9 CC(=O)N[C@....
34 4FMH - GAL SIA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GXB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 GXB 1 1
2 423 0.403974 0.949367
Similar Ligands (3D)
Ligand no: 1; Ligand: GXB; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4U60; Ligand: SIA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4u60.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4U60; Ligand: BGC GAL SIA NGA GAL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4u60.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4U60; Ligand: BGC GAL SIA NGA GAL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4u60.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4U60; Ligand: GAL SIA NGA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4u60.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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