Structure of PDB 7mav Chain A Binding Site BS01

Receptor Information

>7mav Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: YVY
• InChI: InChI=1S/C31H39N5O6/c1-3-18-42-19-16-28(38)34-26(20-23-11-6-4-7-12-23)29(39)36-27(21-24-13-8-5-9-14-24)30(40)35-25(22(2)37)15-10-17-33-31(32)41/h1,4-9,11-14,25-27H,10,15-21H2,2H3,(H,34,38)(H,35,40)(H,36,39)(H3,32,33,41)/t25-,26+,27-/m0/s1
• InChIKey: VYPOUUBVMAOAGP-VJGNERBWSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(=O)C(CCCNC(=O)N)NC(=O)C(Cc1ccccc1)NC(=O)C(Cc2ccccc2)NC(=O)CCOCC#C
  OpenEye OEToolkits 2.0.7: CC(=O)[C@H](CCCNC(=O)N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C
  CACTVS 3.385: CC(=O)[C@H](CCCNC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C
  ACDLabs 12.01: CC(=O)C(CCCNC(N)=O)NC(=O)C(NC(=O)C(Cc1ccccc1)NC(=O)CCOCC#C)Cc1ccccc1
  CACTVS 3.385: CC(=O)[CH](CCCNC(N)=O)NC(=O)[CH](Cc1ccccc1)NC(=O)[CH](Cc2ccccc2)NC(=O)CCOCC#C
• Formula: C31 H39 N5 O6
• Name: N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-(carbamoylamino)-2-oxohexan-3-yl]-L-phenylalaninamide
• PDB chain: 7mav Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mav SARS-CoV-2 Main Protease (Mpro) in Complex with Covalent Inhibitor dFFCit-yne
• Resolution: 1.91 Å
• Binding residue (original residue number in PDB): T24 T25 T26 H41 M49 G143 C145 M165 E166 R188 Q189
• Binding residue (residue number reindexed from 1): T24 T25 T26 H41 M49 G143 C145 M165 E166 R188 Q189
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  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.-
  3.4.22.69: SARS coronavirus main proteinase.
  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:7mav, PDBe:7mav, PDBj:7mav
• PDBsum: 7mav
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)