Structure of PDB 5rmi Chain A Binding Site BS01

Receptor Information
>5rmi Chain A (length=572) 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]
AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVC
NAPGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKVTDFNA
IATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVL
SDRELHLSWEVGKPRPPLNRNYVFTGYQIGEYTFEKDAVVYRGTTTYKLN
VGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQ
KVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEK
ALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADI
VVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAPRTLLTKGTLEPE
YFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQ
CFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNA
VASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKV
GILCIMSDRDLYDKLQFTSLEI
Ligand information
Ligand IDSTV
InChIInChI=1S/C10H13NO4S/c1-2-16(12,13)11-6-8-3-4-9-10(5-8)15-7-14-9/h3-5,11H,2,6-7H2,1H3
InChIKeyUKPLBUIFSDRLEZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC[S](=O)(=O)NCc1ccc2OCOc2c1
OpenEye OEToolkits 2.0.6CCS(=O)(=O)NCc1ccc2c(c1)OCO2
FormulaC10 H13 N O4 S
Name~{N}-(1,3-benzodioxol-5-ylmethyl)ethanesulfonamide
ChEMBL
DrugBank
ZINCZINC000000054604
PDB chain5rmi Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rmi Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.116 Å
Binding residue
(original residue number in PDB)		R303 L352
Binding residue
(residue number reindexed from 1)		R283 L332
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:0004386 helicase activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding

View graph for
Molecular Function
External links
PDB RCSB:5rmi, PDBe:5rmi, PDBj:5rmi
PDBsum5rmi
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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