Structure of PDB 5ret Chain A Binding Site BS01

Receptor Information
>5ret Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT
Ligand information
Ligand IDT47
InChIInChI=1S/C13H17ClN2O/c1-11(17)16-7-5-15(6-8-16)10-12-3-2-4-13(14)9-12/h2-4,9H,5-8,10H2,1H3
InChIKeyOACABXAYQRNFDV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(=O)N1CCN(CC1)Cc2cccc(c2)Cl
ACDLabs 12.01N1(CCN(C(C)=O)CC1)Cc2cccc(c2)Cl
CACTVS 3.385CC(=O)N1CCN(CC1)Cc2cccc(Cl)c2
FormulaC13 H17 Cl N2 O
Name1-{4-[(3-chlorophenyl)methyl]piperazin-1-yl}ethan-1-one
ChEMBL
DrugBank
ZINC
PDB chain5ret Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ret Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Resolution1.68 Å
Binding residue
(original residue number in PDB)		H41 M49 G143 C145 M165 D187 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 G143 C145 M165 D187 Q189
Annotation score1
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5ret, PDBe:5ret, PDBj:5ret
PDBsum5ret
PubMed33028810
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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