Structure of PDB 7lmf Chain B Binding Site BS01

Receptor Information
>7lmf Chain B (length=305) 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
SGVTF
Ligand information
Ligand IDY6G
InChIInChI=1S/C22H18N6OS/c29-22(13-28-21-4-2-1-3-19(21)25-26-28)27(12-16-9-10-30-14-16)18-7-5-17(6-8-18)20-11-23-15-24-20/h1-11,14-15H,12-13H2,(H,23,24)
InChIKeyXZJQABWECIWHRU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc2c(c1)nnn2CC(=O)N(Cc3ccsc3)c4ccc(cc4)c5c[nH]cn5
CACTVS 3.385O=C(Cn1nnc2ccccc12)N(Cc3cscc3)c4ccc(cc4)c5c[nH]cn5
FormulaC22 H18 N6 O S
Name2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-imidazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide
ChEMBLCHEMBL5092107
DrugBank
ZINC
PDB chain7lmf Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7lmf Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).
Resolution2.2 Å
Binding residue
(original residue number in PDB)		T25 H41 C44 M49 F140 L141 C145 H163 M165 E166 R188 Q189
Binding residue
(residue number reindexed from 1)		T25 H41 C44 M49 F140 L141 C145 H163 M165 E166 R188 Q189
Annotation score1
Binding affinityBindingDB: IC50=60nM,EC50=1750nM
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:7lmf, PDBe:7lmf, PDBj:7lmf
PDBsum7lmf
PubMed34347470
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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