Structure of PDB 8ift Chain A Binding Site BS01

Receptor Information
>8ift Chain A (length=306) 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
SGVTFQ
Ligand information
Ligand IDOZB
InChIInChI=1S/C24H34FN5O4S2/c1-22(2,3)17(29-21(34)23(25)5-6-23)20(33)30-13-24(35-8-9-36-24)11-16(30)19(32)28-15(12-26)10-14-4-7-27-18(14)31/h14-17H,4-11,13H2,1-3H3,(H,27,31)(H,28,32)(H,29,34)/t14-,15-,16-,17+/m0/s1
InChIKeyRIKAUFAETQRQJH-LUKYLMHMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)(C)[C@@H](C(=O)N1CC2(C[C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)SCCS2)NC(=O)C4(CC4)F
OpenEye OEToolkits 2.0.7CC(C)(C)C(C(=O)N1CC2(CC1C(=O)NC(CC3CCNC3=O)C#N)SCCS2)NC(=O)C4(CC4)F
CACTVS 3.385CC(C)(C)[CH](NC(=O)C1(F)CC1)C(=O)N2CC3(C[CH]2C(=O)N[CH](C[CH]4CCNC4=O)C#N)SCCS3
CACTVS 3.385CC(C)(C)[C@H](NC(=O)C1(F)CC1)C(=O)N2CC3(C[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)C#N)SCCS3
FormulaC24 H34 F N5 O4 S2
Name(8S)-N-[(1S)-1-cyano-2-[(3S)-2-oxidanylidenepyrrolidin-3-yl]ethyl]-7-[(2S)-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8ift 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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PDB8ift Discovery of oral simnotrelvir, an approved SARS-CoV-2 3C-like protease inhibitor for the treatment of COVID-19
Resolution1.8 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 C145 H163 H164 M165 E166 L167 D187 R188 Q189 Q192
Binding residue
(residue number reindexed from 1)
H41 M49 F140 C145 H163 H164 M165 E166 L167 D187 R188 Q189 Q192
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

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Molecular Function

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Biological Process
External links
PDB RCSB:8ift, PDBe:8ift, PDBj:8ift
PDBsum8ift
PubMed37833261
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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