Structure of PDB 7gdo Chain A Binding Site BS01

Receptor Information
>7gdo 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 IDMVR
InChIInChI=1S/C23H21N5O/c1-27-14-11-20(26-27)17-28(23(29)15-18-5-4-12-24-16-18)21-9-7-19(8-10-21)22-6-2-3-13-25-22/h2-14,16H,15,17H2,1H3
InChIKeySMTCZNNYBUKPMF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cn1ccc(CN(C(=O)Cc2cccnc2)c3ccc(cc3)c4ccccn4)n1
OpenEye OEToolkits 2.0.7Cn1ccc(n1)CN(c2ccc(cc2)c3ccccn3)C(=O)Cc4cccnc4
ACDLabs 12.01Cn1ccc(CN(C(=O)Cc2cccnc2)c2ccc(cc2)c2ccccn2)n1
FormulaC23 H21 N5 O
NameN-[(1-methyl-1H-pyrazol-3-yl)methyl]-2-(pyridin-3-yl)-N-[4-(pyridin-2-yl)phenyl]acetamide
ChEMBL
DrugBank
ZINC
PDB chain7gdo 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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PDB7gdo Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
Resolution1.756 Å
Binding residue
(original residue number in PDB)		T25 H41 C44 M49 F140 L141 C145 H163 M165 E166 D187
Binding residue
(residue number reindexed from 1)		T25 H41 C44 M49 F140 L141 C145 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
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Biological Process
External links
PDB RCSB:7gdo, PDBe:7gdo, PDBj:7gdo
PDBsum7gdo
PubMed37943932
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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