Structure of PDB 5rt0 Chain A Binding Site BS01

Receptor Information
>5rt0 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 ID4BL
InChIInChI=1S/C10H9NO2/c1-6-2-3-7-5-9(10(12)13)11-8(7)4-6/h2-5,11H,1H3,(H,12,13)
InChIKeyZKGSVVHFMZASJS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=C(O)c2cc1ccc(cc1n2)C
OpenEye OEToolkits 1.7.0Cc1ccc2cc([nH]c2c1)C(=O)O
CACTVS 3.352Cc1ccc2cc([nH]c2c1)C(O)=O
FormulaC10 H9 N O2
Name6-methyl-1H-indole-2-carboxylic acid
ChEMBLCHEMBL596007
DrugBank
ZINCZINC000002582714
PDB chain5rt0 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5rt0 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)		G8 N20
Binding residue
(residue number reindexed from 1)		G6 N18
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:5rt0, PDBe:5rt0, PDBj:5rt0
PDBsum5rt0
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]