Structure of PDB 7n8c Chain A Binding Site BS01

Receptor Information
>7n8c Chain A (length=306) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ
Ligand information
Ligand IDYD1
InChIInChI=1S/C15H14Cl2N4O3/c16-10-2-1-9(7-11(10)17)20-3-5-21(6-4-20)14(23)12-8-13(22)19-15(24)18-12/h1-2,7-8H,3-6H2,(H2,18,19,22,24)
InChIKeyXREZIAMDGRLMGZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(c(cc1N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3)Cl)Cl
CACTVS 3.385Clc1ccc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3
FormulaC15 H14 Cl2 N4 O3
Name6-[4-(3,4-dichlorophenyl)piperazin-1-yl]carbonyl-1~{H}-pyrimidine-2,4-dione
ChEMBLCHEMBL5082224
DrugBank
ZINCZINC000095374297
PDB chain7n8c 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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PDB7n8c Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		H41 M49 Y54 F140 N142 G143 C145 H163 E166 H172 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 Y54 F140 N142 G143 C145 H163 E166 H172 D187 R188 Q189
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:7n8c, PDBe:7n8c, PDBj:7n8c
PDBsum7n8c
PubMed34705466
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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