Structure of PDB 5sop Chain A Binding Site BS01

Receptor Information
>5sop 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 IDRYI
InChIInChI=1S/C14H18N4O2S/c19-21(20)7-4-14(9-21)3-1-6-18(8-14)13-11-2-5-15-12(11)16-10-17-13/h2,5,10H,1,3-4,6-9H2,(H,15,16,17)/t14-/m1/s1
InChIKeyCIGPPCNTUJESTR-CQSZACIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=[S]1(=O)CC[C@@]2(CCCN(C2)c3ncnc4[nH]ccc34)C1
OpenEye OEToolkits 2.0.7c1c[nH]c2c1c(ncn2)N3CCCC4(C3)CCS(=O)(=O)C4
ACDLabs 12.01O=S1(=O)CCC2(CCCN(C2)c2ncnc3[NH]ccc32)C1
CACTVS 3.385O=[S]1(=O)CC[C]2(CCCN(C2)c3ncnc4[nH]ccc34)C1
OpenEye OEToolkits 2.0.7c1c[nH]c2c1c(ncn2)N3CCC[C@]4(C3)CCS(=O)(=O)C4
FormulaC14 H18 N4 O2 S
Name(5R)-7-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2lambda~6~-thia-7-azaspiro[4.5]decane-2,2-dione
ChEMBL
DrugBank
ZINC
PDB chain5sop 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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PDB5sop 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 V49 A129 G130 F156 L160
Binding residue
(residue number reindexed from 1)		I21 V47 A127 G128 F154 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:5sop, PDBe:5sop, PDBj:5sop
PDBsum5sop
PubMed36598939
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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