Structure of PDB 5s24 Chain A Binding Site BS01

Receptor Information
>5s24 Chain A (length=165) 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]
SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL
Ligand information
Ligand IDWRM
InChIInChI=1S/C10H11N3O/c1-11-10(14)6-13-7-12-8-4-2-3-5-9(8)13/h2-5,7H,6H2,1H3,(H,11,14)
InChIKeyFLYQCADZXXOQSG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CNC(=O)Cn1cnc2ccccc12
ACDLabs 12.01n1(CC(=O)NC)cnc2ccccc12
OpenEye OEToolkits 2.0.7CNC(=O)Cn1cnc2c1cccc2
FormulaC10 H11 N3 O
Name2-(1H-benzimidazol-1-yl)-N-methylacetamide
ChEMBL
DrugBank
ZINCZINC000007454071
PDB chain5s24 Chain A Residue 201 [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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PDB5s24 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.14 Å
Binding residue
(original residue number in PDB)		D22 V24 A52 F156
Binding residue
(residue number reindexed from 1)		D18 V20 A48 F152
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:5s24, PDBe:5s24, PDBj:5s24
PDBsum5s24
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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