Structure of PDB 7m04 Chain B Binding Site BS02

Receptor Information
>7m04 Chain B (length=298) 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]
FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Ligand information
Ligand IDYM1
InChIInChI=1S/C21H24F5N3O8S/c1-8(2)5-11(29-21(33)37-7-10-13(22)15(24)17(26)16(25)14(10)23)19(31)28-12(20(32)38(34,35)36)6-9-3-4-27-18(9)30/h3-4,8-9,11-12,20,32H,5-7H2,1-2H3,(H,27,30)(H,28,31)(H,29,33)(H,34,35,36)/t9-,11-,12-,20-/m0/s1
InChIKeyVNVWDEQECYLCMA-JJDHJZHUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F
CACTVS 3.385CC(C)C[C@H](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[C@@H](C[C@@H]2C=CNC2=O)[C@@H](O)[S](O)(=O)=O
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F
CACTVS 3.385CC(C)C[CH](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[CH](C[CH]2C=CNC2=O)[CH](O)[S](O)(=O)=O
ACDLabs 12.01O=C1NC=CC1CC(NC(=O)C(CC(C)C)NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(O)S(=O)(=O)O
FormulaC21 H24 F5 N3 O8 S
Name(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid
ChEMBL
DrugBank
ZINC
PDB chain7m04 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7m04 Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H41 N142 C145 H163 H164 M165 E166 D187 Q189
Binding residue
(residue number reindexed from 1)		H39 N140 C143 H161 H162 M163 E164 D185 Q187
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:7m04, PDBe:7m04, PDBj:7m04
PDBsum7m04
PubMed34865476
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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