Structure of PDB 5rv6 Chain A Binding Site BS01

Receptor Information
>5rv6 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 ID0HN
InChIInChI=1S/C8H6O4/c9-8(10)5-1-2-6-7(3-5)12-4-11-6/h1-3H,4H2,(H,9,10)
InChIKeyVDVJGIYXDVPQLP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1C(=O)O)OCO2
CACTVS 3.370OC(=O)c1ccc2OCOc2c1
ACDLabs 12.01O=C(O)c1ccc2OCOc2c1
FormulaC8 H6 O4
Name1,3-benzodioxole-5-carboxylic acid;
benzo[d][1,3]dioxole-5-carboxylic acid
ChEMBLCHEMBL573781
DrugBank
ZINCZINC000000158540
PDB chain5rv6 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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PDB5rv6 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Resolution1.0 Å
Binding residue
(original residue number in PDB)		G48 V49 A52 F156
Binding residue
(residue number reindexed from 1)		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:5rv6, PDBe:5rv6, PDBj:5rv6
PDBsum5rv6
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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