Structure of PDB 4lmc Chain A Binding Site BS01

Receptor Information

>4lmc Chain A (length=132) Species: 31631 (Human coronavirus OC43)

EFNVVPYYSWFSGITQFQKGKEFEFVEGQGVPIAPGVPATEAKGYWYRHN
RRSFKTADGQLLPRWYFYYLGTGPHAKDQYGTDIDGVYWVASNQADVNTP
ADIVDRDPSSDEAIPTRFPPGTVLPQGYYIEG

Ligand information

• Ligand ID: C5P
• InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: IERHLVCPSMICTF-XVFCMESISA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
• Formula: C9 H14 N3 O8 P
• Name: CYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL307679
• DrugBank: DB03403
• ZINC: ZINC000003861744
• PDB chain: 4lmc Chain A Residue 200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4lmc Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target
• Resolution: 1.742 Å
• Binding residue (original residue number in PDB): F57 P61 Y62 S64 F66 R122 Y124 Y126 R164 A171 E189
• Binding residue (residue number reindexed from 1): F2 P6 Y7 S9 F11 R64 Y66 Y68 R106 A113 E131
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Cellular Component

• GO:0019013 viral nucleocapsid

External links

• PDB: RCSB:4lmc, PDBe:4lmc, PDBj:4lmc
• PDBsum: 4lmc
• PubMed: 24564608
• UniProt: P33469|NCAP_CVHOC Nucleoprotein (Gene Name=N)