Structure of PDB 7rm2 Chain A Binding Site BS01

Receptor Information
>7rm2 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 ID5YJ
InChIInChI=1S/C16H16Cl2N4O3/c1-9-11(17)6-10(7-12(9)18)21-2-4-22(5-3-21)15(24)13-8-14(23)20-16(25)19-13/h6-8H,2-5H2,1H3,(H2,19,20,23,25)
InChIKeyHKYIVHLRSLTYKM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(C1=CC(=O)NC(=O)N1)N1CCN(CC1)c1cc(Cl)c(C)c(Cl)c1
CACTVS 3.385Cc1c(Cl)cc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3
OpenEye OEToolkits 2.0.7Cc1c(cc(cc1Cl)N2CCN(CC2)C(=O)C3=CC(=O)NC(=O)N3)Cl
FormulaC16 H16 Cl2 N4 O3
Name6-[4-(3,5-dichloro-4-methylphenyl)piperazine-1-carbonyl]pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL5086216
DrugBank
ZINC
PDB chain7rm2 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7rm2 Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H41 N142 C145 H163 E166 H172 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 N142 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.-
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

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Molecular Function
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Biological Process
External links
PDB RCSB:7rm2, PDBe:7rm2, PDBj:7rm2
PDBsum7rm2
PubMed34705466
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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