Structure of PDB 8h3k Chain A Binding Site BS02

Receptor Information
>8h3k Chain A (length=302) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMF
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMVLPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG
Ligand information
Ligand IDVIB
InChIInChI=1S/C12H17N4OS/c1-8-11(3-4-17)18-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7,17H,3-4,6H2,1-2H3,(H2,13,14,15)/q+1
InChIKeyJZRWCGZRTZMZEH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04n1c(c(cnc1C)C[n+]2c(c(sc2)CCO)C)N
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO
FormulaC12 H17 N4 O S
Name3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM;
THIAMIN;
VITAMIN B1
ChEMBLCHEMBL1547
DrugBankDB00152
ZINCZINC000000049153
PDB chain8h3k Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8h3k Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		S46 Q189
Binding residue
(residue number reindexed from 1)		S46 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:8h3k, PDBe:8h3k, PDBj:8h3k
PDBsum8h3k
PubMed37696289
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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