Structure of PDB 5s4e Chain A Binding Site BS01

Receptor Information
>5s4e 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 IDW3M
InChIInChI=1S/C4H3N3/c5-1-4-2-6-3-7-4/h2-3H,(H,6,7)
InChIKeyNWVGXXPWOYZODV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1c([nH]cn1)C#N
ACDLabs 12.01n1cncc1C#N
CACTVS 3.385N#Cc1[nH]cnc1
FormulaC4 H3 N3
Name1H-imidazole-5-carbonitrile
ChEMBL
DrugBank
ZINCZINC000026898378
PDB chain5s4e Chain A Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5s4e Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.07 Å
Binding residue
(original residue number in PDB)		D22 V49 A52 F156
Binding residue
(residue number reindexed from 1)		D18 V45 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:5s4e, PDBe:5s4e, PDBj:5s4e
PDBsum5s4e
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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