Structure of PDB 5soy Chain A Binding Site BS01

Receptor Information
>5soy 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 IDWXS
InChIInChI=1S/C10H8N4O3S/c1-5-6(17-10(15)16-5)2-18-9-7-8(12-3-11-7)13-4-14-9/h3-4H,2H2,1H3,(H,11,12,13,14)
InChIKeyIKONPSAKEQUJQO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1=C(OC(=O)O1)CSc2c3c([nH]cn3)ncn2
CACTVS 3.385CC1=C(CSc2ncnc3[nH]cnc23)OC(=O)O1
ACDLabs 12.01c2(c1c(ncn1)ncn2)SCC3=C(C)OC(=O)O3
FormulaC10 H8 N4 O3 S
Name4-methyl-5-{[(9H-purin-6-yl)sulfanyl]methyl}-2H-1,3-dioxol-2-one
ChEMBL
DrugBank
ZINCZINC000222377450
PDB chain5soy 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]
PDB5soy Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
Resolution1.05 Å
Binding residue
(original residue number in PDB)		I23 A38 G48 V49 A154 F156
Binding residue
(residue number reindexed from 1)		I21 A36 G46 V47 A152 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:5soy, PDBe:5soy, PDBj:5soy
PDBsum5soy
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]