Structure of PDB 5run Chain A Binding Site BS01

Receptor Information
>5run 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 IDEXB
InChIInChI=1S/C10H10N2O2/c13-10(14)5-6-12-7-11-8-3-1-2-4-9(8)12/h1-4,7H,5-6H2,(H,13,14)
InChIKeyXKGRXBQGCQJOHQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CCn1cnc2ccccc12
ACDLabs 10.04O=C(O)CCn1c2ccccc2nc1
OpenEye OEToolkits 1.5.0c1ccc2c(c1)ncn2CCC(=O)O
FormulaC10 H10 N2 O2
Name3-(1H-benzimidazol-1-yl)propanoic acid
ChEMBLCHEMBL3133889
DrugBank
ZINCZINC000000194295
PDB chain5run 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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PDB5run 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)		G130 V155 F156 D157 L160
Binding residue
(residue number reindexed from 1)		G128 V153 F154 D155 L158
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:5run, PDBe:5run, PDBj:5run
PDBsum5run
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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