Structure of PDB 7gs5 Chain B Binding Site BS02

Receptor Information
>7gs5 Chain B (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 ID0TI
InChIInChI=1S/C8H6FNO2/c9-4-1-2-6-5(3-4)7(11)8(12)10-6/h1-3,7,11H,(H,10,12)/t7-/m1/s1
InChIKeyXYDTZHMQTYEJQN-SSDOTTSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc2c(cc1F)C(C(=O)N2)O
CACTVS 3.385O[C@H]1C(=O)Nc2ccc(F)cc12
OpenEye OEToolkits 1.7.6c1cc2c(cc1F)[C@H](C(=O)N2)O
CACTVS 3.385O[CH]1C(=O)Nc2ccc(F)cc12
ACDLabs 12.01c2cc1NC(=O)C(O)c1cc2F
FormulaC8 H6 F N O2
Name(3R)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
ChEMBL
DrugBank
ZINCZINC000100380560
PDB chain7gs5 Chain B Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7gs5 Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Resolution1.88 Å
Binding residue
(original residue number in PDB)		R40 H41 C44 P52 Y54 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		R40 H41 C44 P52 Y54 D187 R188 Q189
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:7gs5, PDBe:7gs5, PDBj:7gs5
PDBsum7gs5
PubMed38289714
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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