Structure of PDB 5s2n Chain B Binding Site BS01

Receptor Information
>5s2n 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 IDGWY
InChIInChI=1S/C10H14ClN3O/c1-14(5-8-2-3-15-6-8)10-9(11)4-12-7-13-10/h4,7-8H,2-3,5-6H2,1H3/t8-/m0/s1
InChIKeyOYKZBUOZAYBEHE-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(CC1CCOC1)c2c(cncn2)Cl
CACTVS 3.385CN(C[C@@H]1CCOC1)c2ncncc2Cl
OpenEye OEToolkits 2.0.6CN(C[C@@H]1CCOC1)c2c(cncn2)Cl
CACTVS 3.385CN(C[CH]1CCOC1)c2ncncc2Cl
FormulaC10 H14 Cl N3 O
Name5-chloranyl-~{N}-methyl-~{N}-[[(3~{S})-oxolan-3-yl]methyl]pyrimidin-4-amine
ChEMBL
DrugBank
ZINCZINC000097166124
PDB chain5s2n Chain A Residue 501 [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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PDB5s2n Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.133 Å
Binding residue
(original residue number in PDB)		Q107 L108 S111
Binding residue
(residue number reindexed from 1)		Q107 L108 S111
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:5s2n, PDBe:5s2n, PDBj:5s2n
PDBsum5s2n
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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