Structure of PDB 4pot Chain J Binding Site BS02

Receptor Information

>4pot Chain J (length=272) Species: 943908 (Human polyomavirus 9)

VEVLEVRTGPDAITQIEAYLNPRMGNNNPTDELYGYSADINVASSKASDN
PNATTLPTYSVAVIKLPMLNEDMTCDTLLMWEAVSVKTEVMGISSLVNLH
QGGKYIYGSSSGTIPVQGTTLHMFSVGGEPLELQGLVASSTTTYPTDMVT
IKNMKPVNQALDPNAKALLDKDGKYPVEVWSPDPSKNENTRYYGSFTGGA
TTPPVMQFTNSVTTVLLDENGVGPLCKGDKLFLSAVDIVGIHTNYSESQN
WRGLPRYFNVTLRKRVVKNPYP

Ligand information

• Ligand ID: NGC
• InChI: InChI=1S/C11H19NO10/c13-2-5(16)8(18)9-7(12-6(17)3-14)4(15)1-11(21,22-9)10(19)20/h4-5,7-9,13-16,18,21H,1-3H2,(H,12,17)(H,19,20)/t4-,5+,7+,8+,9+,11+/m0/s1
• InChIKey: FDJKUWYYUZCUJX-VTERZIIISA-N
• SMILES:
  CACTVS 3.370: OC[C@@H](O)[C@@H](O)[C@@H]1O[C@](O)(C[C@H](O)[C@H]1NC(=O)CO)C(O)=O
  OpenEye OEToolkits 1.7.2: C1[C@@H]([C@H]([C@@H](O[C@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)NC(=O)CO)O
  OpenEye OEToolkits 1.7.2: C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)NC(=O)CO)O
  CACTVS 3.370: OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1NC(=O)CO)C(O)=O
  ACDLabs 12.01: O=C(O)C1(O)OC(C(NC(=O)CO)C(O)C1)C(O)C(O)CO
• Formula: C11 H19 N O10
• Name: N-glycolyl-alpha-neuraminic acid;
  N-glycolylneuraminic acid;
  sialic acid;
  3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
• ZINC: ZINC000004096098
• PDB chain: 4pot Chain T Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4pot Crystallographic and glycan microarray analysis of human polyomavirus 9 VP1 identifies N-glycolyl neuraminic acid as a receptor candidate.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): L65 Y68 D71 Q133 G134 H274 N276 Y277 N282
• Binding residue (residue number reindexed from 1): L33 Y36 D39 Q101 G102 H242 N244 Y245 N250
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:4pot, PDBe:4pot, PDBj:4pot
• PDBsum: 4pot
• PubMed: 24648448
• UniProt: E9NQ90