Structure of PDB 8sxr Chain B Binding Site BS01

Receptor Information
>8sxr Chain B (length=305) 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
SGVTF
Ligand information
Ligand IDWZK
InChIInChI=1S/C24H22ClN3O2S/c1-27(2)19-6-8-20(9-7-19)28(14-21-11-18(25)15-31-21)23(30)10-17-13-26-12-16-4-3-5-22(29)24(16)17/h3-9,11-13,15,29H,10,14H2,1-2H3
InChIKeyMFBXSZVUWIECDS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1cc(CN(C(=O)Cc2cncc3cccc(O)c32)c2ccc(cc2)N(C)C)sc1
OpenEye OEToolkits 2.0.7CN(C)c1ccc(cc1)N(Cc2cc(cs2)Cl)C(=O)Cc3cncc4c3c(ccc4)O
CACTVS 3.385CN(C)c1ccc(cc1)N(Cc2scc(Cl)c2)C(=O)Cc3cncc4cccc(O)c34
FormulaC24 H22 Cl N3 O2 S
NameN-[(4-chlorothiophen-2-yl)methyl]-N-[4-(dimethylamino)phenyl]-2-(5-hydroxyisoquinolin-4-yl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain8sxr Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8sxr A novel class of broad-spectrum active-site-directed 3C-like protease inhibitors with nanomolar antiviral activity against highly immune-evasive SARS-CoV-2 Omicron subvariants.
Resolution2.114 Å
Binding residue
(original residue number in PDB)		H41 M49 F140 L141 N142 S144 C145 H163 H164 M165 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 F140 L141 N142 S144 C145 H163 H164 M165 D187 R188 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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:8sxr, PDBe:8sxr, PDBj:8sxr
PDBsum8sxr
PubMed37555275
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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