Structure of PDB 5s2u Chain B Binding Site BS01

Receptor Information
>5s2u 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 IDVXD
InChIInChI=1S/C9H11ClN2O/c1-6-7(10)3-2-4-8(6)12-9(13)5-11/h2-4H,5,11H2,1H3,(H,12,13)
InChIKeyFPQHYOUXKZRHSA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(Cl)cccc1NC(=O)CN
OpenEye OEToolkits 2.0.7Cc1c(cccc1Cl)NC(=O)CN
ACDLabs 12.01N(C(=O)CN)c1cccc(c1C)Cl
FormulaC9 H11 Cl N2 O
NameN-(3-chloro-2-methylphenyl)glycinamide
ChEMBL
DrugBank
ZINCZINC000003399182
PDB chain5s2u Chain B Residue 601 [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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PDB5s2u Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.034 Å
Binding residue
(original residue number in PDB)		N40 K44
Binding residue
(residue number reindexed from 1)		N40 K44
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:5s2u, PDBe:5s2u, PDBj:5s2u
PDBsum5s2u
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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