Structure of PDB 7gcd Chain A Binding Site BS01

Receptor Information
>7gcd 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 IDLCU
InChIInChI=1S/C14H18N2O/c1-9-2-3-15-8-13(9)16-14(17)6-10-4-11-7-12(11)5-10/h2-3,8,10-12H,4-7H2,1H3,(H,16,17)/t10-,11+,12-
InChIKeyWEHZCBNACMTKKE-ZSBIGDGJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1ccncc1NC(=O)CC2CC3CC3C2
CACTVS 3.385Cc1ccncc1NC(=O)CC2C[C@@H]3C[C@@H]3C2
CACTVS 3.385Cc1ccncc1NC(=O)CC2C[CH]3C[CH]3C2
OpenEye OEToolkits 2.0.7Cc1ccncc1NC(=O)CC2C[C@H]3C[C@H]3C2
ACDLabs 12.01O=C(Nc1cnccc1C)CC1CC2CC2C1
FormulaC14 H18 N2 O
Name2-[(1R,3s,5S)-bicyclo[3.1.0]hexan-3-yl]-N-(4-methylpyridin-3-yl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain7gcd 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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PDB7gcd Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.811 Å
Binding residue
(original residue number in PDB)		H41 M49 F140 L141 H163 M165 E166 D187
Binding residue
(residue number reindexed from 1)		H41 M49 F140 L141 H163 M165 E166 D187
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:7gcd, PDBe:7gcd, PDBj:7gcd
PDBsum7gcd
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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