Structure of PDB 6esb Chain 1 Binding Site BS01

Receptor Information
>6esb Chain 1 (length=347) Species: 1891762 (Betapolyomavirus hominis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKKPKEPVQVPKLLIKGGVEVLEVKTGVDAITEVECFLNPEMGDPDENLR
GFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAV
TVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQG
VLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPS
RNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSA
ADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKNPYPISFLLSDLINRRT
QRVDGQPMYGMESQVEEVRVFDGTERLPGDPDMIRYIDKQGQLQTKM
Ligand information
Ligand IDSIA
InChIInChI=1S/C11H19NO9/c1-4(14)12-7-5(15)2-11(20,10(18)19)21-9(7)8(17)6(16)3-13/h5-9,13,15-17,20H,2-3H2,1H3,(H,12,14)(H,18,19)/t5-,6+,7+,8+,9+,11+/m0/s1
InChIKeySQVRNKJHWKZAKO-YRMXFSIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
OpenEye OEToolkits 1.5.0CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
OpenEye OEToolkits 1.5.0CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
CACTVS 3.341CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O
FormulaC11 H19 N O9
NameN-acetyl-alpha-neuraminic acid;
N-acetylneuraminic acid;
sialic acid;
alpha-sialic acid;
O-SIALIC ACID
ChEMBLCHEMBL1234621
DrugBankDB03721
ZINCZINC000004081651
PDB chain6esb Chain A Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6esb The Structure of an Infectious Human Polyomavirus and Its Interactions with Cellular Receptors.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		L67 N272 S274 T276 Q278
Binding residue
(residue number reindexed from 1)		L54 N259 S261 T263 Q265
Annotation score4
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005198 structural molecule activity
Biological Process
GO:0019062 virion attachment to host cell
GO:0046718 symbiont entry into host cell
GO:0075513 caveolin-mediated endocytosis of virus by host cell
Cellular Component
GO:0019028 viral capsid
GO:0039620 T=7 icosahedral viral capsid
GO:0042025 host cell nucleus

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6esb, PDBe:6esb, PDBj:6esb
PDBsum6esb
PubMed29706532
UniProtP03088|VP1_POVBK Major capsid protein VP1

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