Structure of PDB 5rt6 Chain A Binding Site BS01

Receptor Information
>5rt6 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 ID05R
InChIInChI=1S/C8H6Cl2O2/c9-6-2-1-5(3-7(6)10)4-8(11)12/h1-3H,4H2,(H,11,12)
InChIKeyZOUPGSMSNQLUNW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1cc(c(cc1CC(=O)O)Cl)Cl
ACDLabs 12.01Clc1ccc(cc1Cl)CC(=O)O
CACTVS 3.385OC(=O)Cc1ccc(Cl)c(Cl)c1
FormulaC8 H6 Cl2 O2
Name2-(3,4-dichlorophenyl)ethanoic acid
ChEMBLCHEMBL3116309
DrugBank
ZINCZINC000000156509
PDB chain5rt6 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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PDB5rt6 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)		V49 L126 F132 V155 F156 D157
Binding residue
(residue number reindexed from 1)		V47 L124 F130 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:5rt6, PDBe:5rt6, PDBj:5rt6
PDBsum5rt6
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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