Structure of PDB 5cpz Chain B Binding Site BS03

Receptor Information

>5cpz Chain B (length=280) Species: 47935 (Mouse polyomavirus (strain p16 small-plaque))

GMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLA
TSDTEDSPGNNTLPTWSMAKLQLPMLNCDTLQMWEAVSVKTEVVGSGSLL
DVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYK
EEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNEN
TRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIM
GWRVTRNYDVHHWRGLPRYFKITLRKRWVK

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: 5cpz Chain G Residue 5

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5cpz Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity.
• Resolution: 1.71 Å
• Binding residue (original residue number in PDB): T67 E68 Y72 R77
• Binding residue (residue number reindexed from 1): T35 E36 Y40 R45
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:5cpz, PDBe:5cpz, PDBj:5cpz
• PDBsum: 5cpz
• PubMed: 26474293
• UniProt: P49302|VP1_POVMP Capsid protein VP1