Structure of PDB 8fiv Chain A Binding Site BS01

Receptor Information
>8fiv Chain A (length=301) 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
S
Ligand information
Ligand IDY0I
InChIInChI=1S/C30H28N4O2/c1-22(23-9-4-2-5-10-23)33-30(36)29(26-13-8-20-32-21-26)34(28(35)18-19-31)27-16-14-25(15-17-27)24-11-6-3-7-12-24/h2-17,19-22,29,31H,18H2,1H3,(H,33,36)/t22-,29+/m0/s1
InChIKeyWSBQTFUCGVUNEH-PZGXJGMVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(c1ccccc1)NC(=O)C(c2cccnc2)N(c3ccc(cc3)c4ccccc4)C(=O)CC=N
CACTVS 3.385C[CH](NC(=O)[CH](N(C(=O)CC=N)c1ccc(cc1)c2ccccc2)c3cccnc3)c4ccccc4
OpenEye OEToolkits 2.0.7C[C@@H](c1ccccc1)NC(=O)[C@@H](c2cccnc2)N(c3ccc(cc3)c4ccccc4)C(=O)CC=N
CACTVS 3.385C[C@H](NC(=O)[C@H](N(C(=O)CC=N)c1ccc(cc1)c2ccccc2)c3cccnc3)c4ccccc4
ACDLabs 12.01CC(NC(=O)C(N(C(=O)CC=N)c1ccc(cc1)c1ccccc1)c1cccnc1)c1ccccc1
FormulaC30 H28 N4 O2
Name(3Z)-N-([1,1'-biphenyl]-4-yl)-3-imino-N-[(1R)-2-oxo-2-{[(1S)-1-phenylethyl]amino}-1-(pyridin-3-yl)ethyl]propanamide
ChEMBL
DrugBank
ZINC
PDB chain8fiv Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8fiv Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors.
Resolution2.51 Å
Binding residue
(original residue number in PDB)
H41 C44 M49 F140 L141 N142 G143 C145 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
H41 C44 M49 F140 L141 N142 G143 C145 H164 M165 E166 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

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:8fiv, PDBe:8fiv, PDBj:8fiv
PDBsum8fiv
PubMed37482021
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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