Structure of PDB 5rv3 Chain A Binding Site BS01

Receptor Information
>5rv3 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 IDMYI
InChIInChI=1S/C11H11NO3/c1-15-8-2-3-10-9(5-8)7(6-12-10)4-11(13)14/h2-3,5-6,12H,4H2,1H3,(H,13,14)
InChIKeyCOCNDHOPIHDTHK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0COc1ccc2c(c1)c(c[nH]2)CC(=O)O
CACTVS 3.352COc1ccc2[nH]cc(CC(O)=O)c2c1
FormulaC11 H11 N O3
Name(5-methoxy-1H-indol-3-yl)acetic acid;
5-methoxy-indole acetate
ChEMBLCHEMBL85433
DrugBank
ZINCZINC000000057162
PDB chain5rv3 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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PDB5rv3 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.02 Å
Binding residue
(original residue number in PDB)		G48 L126 G130 I131 F156 D157
Binding residue
(residue number reindexed from 1)		G46 L124 G128 I129 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:5rv3, PDBe:5rv3, PDBj:5rv3
PDBsum5rv3
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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