Structure of PDB 7mlf Chain A Binding Site BS01

Receptor Information
>7mlf 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 IDC7A
InChIInChI=1S/C25H32ClN3O2/c1-25(2,3)19-11-13-21(14-12-19)29(22(30)16-26)23(18-8-7-15-27-17-18)24(31)28-20-9-5-4-6-10-20/h7-8,11-15,17,20,23H,4-6,9-10,16H2,1-3H3,(H,28,31)/t23-/m1/s1
InChIKeyFMBPORSTYBRWAD-HSZRJFAPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC(C)(C)c1ccc(cc1)N(C(=O)CCl)C(c1cccnc1)C(=O)NC1CCCCC1
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([CH](C(=O)NC2CCCCC2)c3cccnc3)C(=O)CCl
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N(C(c2cccnc2)C(=O)NC3CCCCC3)C(=O)CCl
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N([C@H](c2cccnc2)C(=O)NC3CCCCC3)C(=O)CCl
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([C@@H](C(=O)NC2CCCCC2)c3cccnc3)C(=O)CCl
FormulaC25 H32 Cl N3 O2
NameN-(4-tert-butylphenyl)-2-chloro-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]acetamide
ChEMBL
DrugBank
ZINC
PDB chain7mlf 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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PDB7mlf Design, synthesis and in vitro evaluation of novel SARS-CoV-2 3CL pro covalent inhibitors.
Resolution2.6 Å
Binding residue
(original residue number in PDB)
F140 L141 N142 G143 S144 C145 H163 H164 M165 E166
Binding residue
(residue number reindexed from 1)
F140 L141 N142 G143 S144 C145 H163 H164 M165 E166
Annotation score1
Binding affinityBindingDB: IC50=1140nM
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:7mlf, PDBe:7mlf, PDBj:7mlf
PDBsum7mlf
PubMed34995923
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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