Structure of PDB 5ruv Chain B Binding Site BS01

Receptor Information
>5ruv Chain B (length=169) 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]
SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVA
GALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNV
NKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTN
VYLAVFDKNLYDKLVSSFL
Ligand information
Ligand IDW6J
InChIInChI=1S/C10H15N3/c1-2-6-12-10(4-1)13-8-3-5-11-7-9-13/h1-2,4,6,11H,3,5,7-9H2
InChIKeyYIVVBOYHOANILT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C1CNCCN(C1)c2ccccn2
ACDLabs 12.01C2CN(c1ncccc1)CCCN2
OpenEye OEToolkits 2.0.7c1ccnc(c1)N2CCCNCC2
FormulaC10 H15 N3
Name1-(pyridin-2-yl)-1,4-diazepane
ChEMBLCHEMBL4515199
DrugBank
ZINCZINC000019015194
PDB chain5ruv Chain B 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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PDB5ruv 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)		Y42 I69 A70 T71 N72 G73
Binding residue
(residue number reindexed from 1)		Y42 I69 A70 T71 N72 G73
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:5ruv, PDBe:5ruv, PDBj:5ruv
PDBsum5ruv
PubMed33853786
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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