Structure of PDB 5spv Chain A Binding Site BS01

Receptor Information
>5spv 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 IDS7O
InChIInChI=1S/C10H10N4O4/c1-13(5-8(15)16)9(17)6-2-3-7-11-12-10(18)14(7)4-6/h2-4H,5H2,1H3,(H2,12,15,16,18)/p+1
InChIKeyFPESGUDHYYBDOL-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.385CN(CC(O)=O)C(=O)c1ccc2NNC(=O)[n+]2c1
ACDLabs 12.01O=C(O)CN(C)C(=O)c1c[n+]2C(=O)NNc2cc1
OpenEye OEToolkits 2.0.7CN(CC(=O)O)C(=O)c1ccc2[n+](c1)C(=O)NN2
FormulaC10 H11 N4 O4
Name2-[methyl-[(9-oxidanylidene-1$l^{4},7,8-triazabicyclo[4.3.0]nona-1(6),2,4-trien-3-yl)carbonyl]amino]ethanoic acid
ChEMBL
DrugBank
ZINC
PDB chain5spv Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5spv 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)		G48 V49 A52 G130 V155 F156 D157
Binding residue
(residue number reindexed from 1)		G46 V47 A50 G128 V153 F154 D155
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:5spv, PDBe:5spv, PDBj:5spv
PDBsum5spv
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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