Structure of PDB 5s32 Chain A Binding Site BS01

Receptor Information
>5s32 Chain A (length=164) 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
VFDKNLYDKLVSSF
Ligand information
Ligand IDW0V
InChIInChI=1S/C12H15N3O/c1-8(2)12(16)13-7-11-14-9-5-3-4-6-10(9)15-11/h3-6,8H,7H2,1-2H3,(H,13,16)(H,14,15)
InChIKeyKBFKODIOYYFXAF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n1c(CNC(=O)C(C)C)nc2c1cccc2
CACTVS 3.385
OpenEye OEToolkits 2.0.7		CC(C)C(=O)NCc1[nH]c2ccccc2n1
FormulaC12 H15 N3 O
NameN-[(1H-benzimidazol-2-yl)methyl]-2-methylpropanamide
ChEMBL
DrugBank
ZINCZINC000000549915
PDB chain5s32 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5s32 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.166 Å
Binding residue
(original residue number in PDB)		D22 V24 G48 V49 A52
Binding residue
(residue number reindexed from 1)		D18 V20 G44 V45 A48
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:5s32, PDBe:5s32, PDBj:5s32
PDBsum5s32
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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