Structure of PDB 2i2s Chain A Binding Site BS01

Receptor Information

>2i2s Chain A (length=163) Species: 10913 (Porcine rotavirus)

GSLLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPN
VQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFST
PKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRN
QEEKCTEYINHGL

Ligand information

• Ligand ID: MNA
• InChI: InChI=1S/C12H21NO9/c1-5(15)13-8-6(16)3-12(21-2,11(19)20)22-10(8)9(18)7(17)4-14/h6-10,14,16-18H,3-4H2,1-2H3,(H,13,15)(H,19,20)/t6-,7+,8+,9+,10+,12+/m0/s1
• InChIKey: NJRVVFURCKKXOD-MIDKXNQYSA-N
• SMILES:
  CACTVS 3.341: CO[C]1(C[CH](O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)CO)C(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)OC)O
  CACTVS 3.341: CO[C@@]1(C[C@H](O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)CO)C(O)=O
  ACDLabs 10.04: O=C(O)C1(OC)OC(C(O)C(O)CO)C(NC(=O)C)C(O)C1
  OpenEye OEToolkits 1.5.0: CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)OC)O
• Formula: C12 H21 N O9
• Name: 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid;
  2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
• ChEMBL: CHEMBL1213636
• ZINC: ZINC000005884114
• PDB chain: 2i2s Chain A Residue 1000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2i2s Insight into Host Cell Carbohydrate-recognition by Human and Porcine Rotavirus from Crystal Structures of the Virion Spike Associated Carbohydrate-binding Domain (VP8*)
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): R101 H155 Y188 Y189 S190
• Binding residue (residue number reindexed from 1): R40 H94 Y127 Y128 S129
• Annotation score: 1

Gene Ontology

Biological Process

• GO:0019058 viral life cycle

Cellular Component

• GO:0019028 viral capsid

External links

• PDB: RCSB:2i2s, PDBe:2i2s, PDBj:2i2s
• PDBsum: 2i2s
• PubMed: 17306299
• UniProt: P0C6Y8|VP4_ROTP3 Outer capsid protein VP4