Structure of PDB 6x4i Chain A Binding Site BS01

Receptor Information
>6x4i Chain A (length=348) 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]
NMSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTT
LPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHIST
IGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSV
KGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSR
NLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGL
HLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLL
LDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQ
Ligand information
Ligand IDU3P
InChIInChI=1S/C9H13N2O9P/c12-3-4-7(20-21(16,17)18)6(14)8(19-4)11-2-1-5(13)10-9(11)15/h1-2,4,6-8,12,14H,3H2,(H,10,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyFOGRQMPFHUHIGU-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)OP(=O)(O)O)O
ACDLabs 10.04O=C1NC(=O)N(C=C1)C2OC(C(OP(=O)(O)O)C2O)CO
CACTVS 3.341OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)OP(=O)(O)O)O
CACTVS 3.341OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O
FormulaC9 H13 N2 O9 P
Name3'-URIDINEMONOPHOSPHATE
ChEMBLCHEMBL460741
DrugBankDB02714
ZINCZINC000004095646
PDB chain6x4i Chain A Residue 401 [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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PDB6x4i Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		H235 G248 H250 K290 W333 T341
Binding residue
(residue number reindexed from 1)		H236 G249 H251 K291 W334 T342
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:6x4i, PDBe:6x4i, PDBj:6x4i
PDBsum6x4i
PubMed33564093
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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