Structure of PDB 7jyc Chain A Binding Site BS01

Receptor Information
>7jyc 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 IDNNA
InChIInChI=1S/C36H63N5O7S/c1-10-11-15-24(27(42)30(44)37-22-16-17-22)38-29(43)26-25-23(35(25,8)9)20-41(26)31(45)28(33(2,3)4)39-32(46)40-36(18-13-12-14-19-36)21-49(47,48)34(5,6)7/h22-28,42H,10-21H2,1-9H3,(H,37,44)(H,38,43)(H2,39,40,46)/t23-,24-,25-,26-,27+,28+/m0/s1
InChIKeyBZXRATSZUNDEEV-FZFXNXQRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCC[CH](NC(=O)[CH]1[CH]2[CH](CN1C(=O)[CH](NC(=O)NC3(CCCCC3)C[S](=O)(=O)C(C)(C)C)C(C)(C)C)C2(C)C)[CH](O)C(=O)NC4CC4
OpenEye OEToolkits 1.7.0CCCC[C@@H]([C@H](C(=O)NC1CC1)O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)NC4(CCCCC4)CS(=O)(=O)C(C)(C)C
OpenEye OEToolkits 1.7.0CCCCC(C(C(=O)NC1CC1)O)NC(=O)C2C3C(C3(C)C)CN2C(=O)C(C(C)(C)C)NC(=O)NC4(CCCCC4)CS(=O)(=O)C(C)(C)C
CACTVS 3.370CCCC[C@H](NC(=O)[C@@H]1[C@@H]2[C@H](CN1C(=O)[C@@H](NC(=O)NC3(CCCCC3)C[S](=O)(=O)C(C)(C)C)C(C)(C)C)C2(C)C)[C@@H](O)C(=O)NC4CC4
ACDLabs 12.01O=C(N3C(C(=O)NC(CCCC)C(O)C(=O)NC1CC1)C2C(C)(C2C3)C)C(NC(=O)NC4(CS(=O)(=O)C(C)(C)C)CCCCC4)C(C)(C)C
FormulaC36 H63 N5 O7 S
Name(1R,2S,5S)-3-[N-({1-[(tert-butylsulfonyl)methyl]cyclohexyl}carbamoyl)-3-methyl-L-valyl]-N-{(1S)-1-[(1R)-2-(cyclopropylamino)-1-hydroxy-2-oxoethyl]pentyl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide;
Narlaprevir, bound form
ChEMBL
DrugBank
ZINCZINC000098209237
PDB chain7jyc 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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PDB7jyc Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease.
Resolution1.79 Å
Binding residue
(original residue number in PDB)
T26 H41 M49 L141 N142 G143 C145 H164 M165 E166 L167 P168 D187 Q189 T190 A191 Q192
Binding residue
(residue number reindexed from 1)
T26 H41 M49 L141 N142 G143 C145 H164 M165 E166 L167 P168 D187 Q189 T190 A191 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

View graph for
Molecular Function

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Biological Process
External links
PDB RCSB:7jyc, PDBe:7jyc, PDBj:7jyc
PDBsum7jyc
PubMed35842458
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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