Structure of PDB 6fv2 Chain A Binding Site BS01

Receptor Information

>6fv2 Chain A (length=301) Species: 277944 (Human coronavirus NL63)

SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL
IDYDHAYSTMRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKH
VFKTLKPGDSFNILACYEGIASGVFGVNLRTNFTIKGSFINGACGSPGYN
VRNDGTVEFCYLHQIELGSGAHVGSDFTGSVYGNFDDQPSLQVESANLML
SDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGYTSVSSVECYSI
LAAKTGVSVEQLLASIQHLHEGFGGKNILGYSSLCDEFTLAEVVKQMYGV
N

Ligand information

• Ligand ID: D03
• InChI: InChI=1S/C33H36N4O5/c38-29(17-16-23-10-4-1-5-11-23)36-28(20-24-12-6-2-7-13-24)32(41)37-27(21-26-18-19-34-31(26)40)30(39)33(42)35-22-25-14-8-3-9-15-25/h1-17,26-28,30,39H,18-22H2,(H,34,40)(H,35,42)(H,36,38)(H,37,41)/b17-16+/t26-,27-,28-,30-/m0/s1
• InChIKey: ZTFAWEJBUOCZIL-NHTHZNHESA-N
• SMILES:
  CACTVS 3.385: O[CH]([CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)C=Cc3ccccc3)C(=O)NCc4ccccc4
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)CC(C(=O)NC(CC2CCNC2=O)C(C(=O)NCc3ccccc3)O)NC(=O)C=Cc4ccccc4
  OpenEye OEToolkits 2.0.6: c1ccc(cc1)C[C@@H](C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](C(=O)NCc3ccccc3)O)NC(=O)/C=C/c4ccccc4
  CACTVS 3.385: O[C@@H]([C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)/C=C/c3ccccc3)C(=O)NCc4ccccc4
• Formula: C33 H36 N4 O5
• Name: (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide
• PDB chain: 6fv2 Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fv2 Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Structure-based design, synthesis, and activity assessment.
• Resolution: 2.95 Å
• Binding residue (original residue number in PDB): V26 H41 I51 F139 N141 G142 A143 C144 H163 E166 D187 Q188 S190
• Binding residue (residue number reindexed from 1): V26 H41 I51 F139 N141 G142 A143 C144 H163 E166 D187 Q188 S190
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.30,IC50>50uM

Enzymatic activity

• Enzyme Commision number: 2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:6fv2, PDBe:6fv2, PDBj:6fv2
• PDBsum: 6fv2
• PubMed: 32045235
• UniProt: P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab (Gene Name=rep)