Structure of PDB 7lme Chain A Binding Site BS01

Receptor Information
>7lme Chain A (length=304) 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
SGVT
Ligand information
Ligand IDY6J
InChIInChI=1S/C23H21N5O2S/c29-22(14-28-21-4-2-1-3-20(21)25-26-28)27(13-16-11-12-31-15-16)19-9-7-18(8-10-19)24-23(30)17-5-6-17/h1-4,7-12,15,17H,5-6,13-14H2,(H,24,30)
InChIKeyOCKMJWOFMCSMEX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)nnn2CC(=O)N(Cc3ccsc3)c4ccc(cc4)NC(=O)C5CC5
CACTVS 3.385O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(NC(=O)C5CC5)cc4
FormulaC23 H21 N5 O2 S
Name~{N}-[4-[2-(benzotriazol-1-yl)ethanoyl-(thiophen-3-ylmethyl)amino]phenyl]cyclopropanecarboxamide
ChEMBLCHEMBL2442081
DrugBank
ZINC
PDB chain7lme 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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PDB7lme Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).
Resolution2.1 Å
Binding residue
(original residue number in PDB)		T24 T25 H41 S46 M49 F140 L141 N142 C145 H163 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		T24 T25 H41 S46 M49 F140 L141 N142 C145 H163 M165 E166 D187 R188 Q189
Annotation score1
Binding affinityBindingDB: EC50=19900nM,IC50=28400nM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7lme, PDBe:7lme, PDBj:7lme
PDBsum7lme
PubMed34347470
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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