Structure of PDB 6fv1 Chain A Binding Site BS01

Receptor Information

>6fv1 Chain A (length=300) Species: 277944 (Human coronavirus NL63)

SGLKKMAQPSGCVERCVVRVCYGSTVLNGVWLGDTVTCPRHVIAPSTTVL
IDYDHAYSTMRLHNFSVSHNGVFLGVVGVTMHGSVLRIKVSQSNVHTPKH
VFKTLKPGDSFNILACYEGIASGVFGVNLRTNFTIKGSFINGACGSPGYN
VRNDGTVEFCYLHQIELGSGAHVGSDFTGSVYGNFDDQPSLQVESANLML
SDNVVAFLYAALLNGCRWWLCSTRVNVDGFNEWAMANGYTSVSSVECYSI
LAAKTGVSVEQLLASIQHLHEGFGGKNILGYSSLCDEFTLAEVVKQMYGV

Ligand information

• Ligand ID: E8E
• InChI: InChI=1S/C30H38N4O5/c1-20(2)17-25(33-26(35)14-13-21-9-5-3-6-10-21)29(38)34-24(18-23-15-16-31-28(23)37)27(36)30(39)32-19-22-11-7-4-8-12-22/h3-14,20,23-25,27,36H,15-19H2,1-2H3,(H,31,37)(H,32,39)(H,33,35)(H,34,38)/b14-13+/t23-,24-,25-,27+/m0/s1
• InChIKey: VGTVWUUFUCDHSP-BXCMFHCISA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](C(=O)NCc2ccccc2)O)NC(=O)/C=C/c3ccccc3
  OpenEye OEToolkits 2.0.6: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C(=O)NCc2ccccc2)O)NC(=O)C=Cc3ccccc3
  CACTVS 3.385: CC(C)C[CH](NC(=O)C=Cc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)C(=O)NCc3ccccc3
  CACTVS 3.385: CC(C)C[C@H](NC(=O)/C=C/c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)C(=O)NCc3ccccc3
• Formula: C30 H38 N4 O5
• Name: (2~{S})-4-methyl-~{N}-[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]-2-[[(~{E})-3-phenylprop-2-enoyl]amino]pentanamide
• PDB chain: 6fv1 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fv1 Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication Structure-based design, synthesis, and activity assessment.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): H41 F139 N141 G142 C144 H163 Q164 I165 E166 P189
• Binding residue (residue number reindexed from 1): H41 F139 N141 G142 C144 H163 Q164 I165 E166 P189
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.97,IC50=1.08uM

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:6fv1, PDBe:6fv1, PDBj:6fv1
• PDBsum: 6fv1
• PubMed: 32045235
• UniProt: P0C6X5|R1AB_CVHNL Replicase polyprotein 1ab (Gene Name=rep)