Structure of PDB 3nxd Chain B Binding Site BS01

Receptor Information

>3nxd Chain B (length=258) Species: 10632 (JC polyomavirus)

EVLEVKTGVDSITEVECFLTPEMGDPDEHLRGFSKSISISDTFESDSPNR
DMLPCYSVARIPLPNLNILMWEAVTLKTEVIGVTSLMNVHSNGQATHDNG
AGKPVQGTSFHFFSVGGEALELQGVLFNYRTKYPDGTIFPKNATVQSQVM
NTEHKAYLDKNKAYPVECWVPDPTRNENTRYFGTLTGGENVPPVLHITNT
ATTVLLDEFGVGPLCKGDNLYLSAVDVCGMFTNRSGSQQWRGLSRYFKVQ
LRKRRVKN

Ligand information

• Ligand ID: SIA
• InChI: InChI=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
• InChIKey: SQVRNKJHWKZAKO-YRMXFSIDSA-N
• SMILES:
  CACTVS 3.341: CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)O
  OpenEye OEToolkits 1.5.0: CC(=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 10.04: O=C(O)C1(O)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  CACTVS 3.341: CC(=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
• Formula: C11 H19 N O9
• Name: N-acetyl-alpha-neuraminic acid;
  N-acetylneuraminic acid;
  sialic acid;
  alpha-sialic acid;
  O-SIALIC ACID
• ChEMBL: CHEMBL1234621
• DrugBank: DB03721
• ZINC: ZINC000004081651
• PDB chain: 3nxd Chain G Residue 5

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nxd Structure-function analysis of the human JC polyomavirus establishes the LSTc pentasaccharide as a functional receptor motif.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): L54 K59 S60 N264 S266 S268 Q270
• Binding residue (residue number reindexed from 1): L30 K35 S36 N233 S235 S237 Q239
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:3nxd, PDBe:3nxd, PDBj:3nxd
• PDBsum: 3nxd
• PubMed: 20951965
• UniProt: P03089|VP1_POVJC Major capsid protein VP1