Structure of PDB 7gc9 Chain A Binding Site BS01

Receptor Information
>7gc9 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 IDL9O
InChIInChI=1S/C14H18N2O/c1-10-4-8-15-9-12(10)16-13(17)11-3-7-14(11)5-2-6-14/h4,8-9,11H,2-3,5-7H2,1H3,(H,16,17)/t11-/m1/s1
InChIKeyXFQCOLJIUXXMKV-LLVKDONJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccncc1NC(=O)[CH]2CCC23CCC3
OpenEye OEToolkits 2.0.7Cc1ccncc1NC(=O)C2CCC23CCC3
ACDLabs 12.01O=C(Nc1cnccc1C)C1CCC21CCC2
CACTVS 3.385
OpenEye OEToolkits 2.0.7		Cc1ccncc1NC(=O)[C@H]2CCC23CCC3
FormulaC14 H18 N2 O
Name(1S)-N-(4-methylpyridin-3-yl)spiro[3.3]heptane-1-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7gc9 Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7gc9 Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.771 Å
Binding residue
(original residue number in PDB)		M49 F140 L141 H163 H164 M165 E166
Binding residue
(residue number reindexed from 1)		M49 F140 L141 H163 H164 M165 E166
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
View graph for
Biological Process
External links
PDB RCSB:7gc9, PDBe:7gc9, PDBj:7gc9
PDBsum7gc9
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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