Structure of PDB 5s48 Chain B Binding Site BS01

Receptor Information
>5s48 Chain B (length=169) 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]
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVA
GALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNV
NKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTN
VYLAVFDKNLYDKLVSSFL
Ligand information
Ligand IDHRZ
InChIInChI=1S/C5H5NO/c7-5-3-1-2-4-6-5/h1-4H,(H,6,7)
InChIKeyUBQKCCHYAOITMY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C1NC=CC=C1
OpenEye OEToolkits 2.0.6C1=CC(=O)NC=C1
FormulaC5 H5 N O
Name1~{H}-pyridin-2-one
ChEMBLCHEMBL662
DrugBank
ZINCZINC000008737707
PDB chain5s48 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5s48 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.074 Å
Binding residue
(original residue number in PDB)		N4 V121 N150 Y152
Binding residue
(residue number reindexed from 1)		N4 V121 N150 Y152
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.-
External links
PDB RCSB:5s48, PDBe:5s48, PDBj:5s48
PDBsum5s48
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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