Structure of PDB 5spm Chain A Binding Site BS01

Receptor Information
>5spm Chain A (length=167) 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]
VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL
Ligand information
Ligand IDS4O
InChIInChI=1S/C13H13N3O5/c1-15-9-6-16(3-2-8(9)12(19)14-15)13(20)10-4-7(17)5-11(18)21-10/h4-5,17H,2-3,6H2,1H3,(H,14,19)
InChIKeyJMIDLJFHIRGERG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1nc(O)c2CCN(Cc12)C(=O)C3=CC(=CC(=O)O3)O
ACDLabs 12.01OC=1C=C(OC(=O)C=1)C(=O)N1Cc2n(C)nc(O)c2CC1
OpenEye OEToolkits 2.0.7Cn1c2c(c(n1)O)CCN(C2)C(=O)C3=CC(=CC(=O)O3)O
FormulaC13 H13 N3 O5
Name4-hydroxy-6-(3-hydroxy-1-methyl-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridine-6-carbonyl)-2H-pyran-2-one
ChEMBL
DrugBank
ZINC
PDB chain5spm 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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PDB5spm Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		D22 V24 G48 V49 A52 F156
Binding residue
(residue number reindexed from 1)		D20 V22 G46 V47 A50 F154
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:5spm, PDBe:5spm, PDBj:5spm
PDBsum5spm
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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