Structure of PDB 5s2e Chain A Binding Site BS01

Receptor Information
>5s2e 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 IDVZM
InChIInChI=1S/C11H11N3O2S/c1-16-9-5-4-8(7-12-9)13-11(15)14-10-3-2-6-17-10/h2-7H,1H3,(H2,13,14,15)
InChIKeyQQTNSKDCQAMODS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccc(NC(=O)Nc2sccc2)cn1
ACDLabs 12.01N(c1cccs1)C(=O)Nc2cnc(cc2)OC
OpenEye OEToolkits 2.0.7COc1ccc(cn1)NC(=O)Nc2cccs2
FormulaC11 H11 N3 O2 S
NameN-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea
ChEMBLCHEMBL1580797
DrugBank
ZINCZINC000000157953
PDB chain5s2e 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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PDB5s2e Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.116 Å
Binding residue
(original residue number in PDB)		D22 G48 A52
Binding residue
(residue number reindexed from 1)		D18 G44 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:5s2e, PDBe:5s2e, PDBj:5s2e
PDBsum5s2e
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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