Structure of PDB 5rv8 Chain A Binding Site BS01

Receptor Information
>5rv8 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 ID8EJ
InChIInChI=1S/C7H8N2O/c1-5-2-3-6(4-9-5)7(8)10/h2-4H,1H3,(H2,8,10)
InChIKeyIJXDURUAYOKSIS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1ccc(cn1)C(=O)N
CACTVS 3.385Cc1ccc(cn1)C(N)=O
FormulaC7 H8 N2 O
Name6-methylpyridine-3-carboxamide
ChEMBLCHEMBL4204179
DrugBank
ZINCZINC000000039575
PDB chain5rv8 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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PDB5rv8 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)		D22 V49 A52 F156
Binding residue
(residue number reindexed from 1)		D20 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:5rv8, PDBe:5rv8, PDBj:5rv8
PDBsum5rv8
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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