Structure of PDB 5ree Chain A Binding Site BS01

Receptor Information
>5ree 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 IDT1M
InChIInChI=1S/C13H19NO/c1-11-13(15)8-5-9-14(11)10-12-6-3-2-4-7-12/h2-4,6-7,11,13,15H,5,8-10H2,1H3/t11-,13+/m1/s1
InChIKeyZFJGRVQFTNBLRP-YPMHNXCESA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H]1[C@@H](O)CCCN1Cc2ccccc2
ACDLabs 12.01c2(CN1C(C)C(CCC1)O)ccccc2
CACTVS 3.385C[CH]1[CH](O)CCCN1Cc2ccccc2
OpenEye OEToolkits 2.0.7C[C@@H]1[C@H](CCCN1Cc2ccccc2)O
OpenEye OEToolkits 2.0.7CC1C(CCCN1Cc2ccccc2)O
FormulaC13 H19 N O
Name(2R,3R)-1-benzyl-2-methylpiperidin-3-ol
ChEMBL
DrugBank
ZINCZINC000107242045
PDB chain5ree 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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PDB5ree Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Resolution1.77 Å
Binding residue
(original residue number in PDB)		P132 T196 T198 N238 E240
Binding residue
(residue number reindexed from 1)		P132 T196 T198 N238 E240
Annotation score1
Binding affinityBindingDB: IC50=99000nM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5ree, PDBe:5ree, PDBj:5ree
PDBsum5ree
PubMed33028810
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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