Structure of PDB 5rmd Chain A Binding Site BS01

Receptor Information
>5rmd 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 IDVWY
InChIInChI=1S/C10H14N2O3S/c1-3-11-10(13)8-4-6-9(7-5-8)12-16(2,14)15/h4-7,12H,3H2,1-2H3,(H,11,13)
InChIKeyGWMALJVYSHCCNB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N(CC)C(c1ccc(cc1)NS(C)(=O)=O)=O
CACTVS 3.385CCNC(=O)c1ccc(N[S](C)(=O)=O)cc1
OpenEye OEToolkits 2.0.7CCNC(=O)c1ccc(cc1)NS(=O)(=O)C
FormulaC10 H14 N2 O3 S
NameN-ethyl-4-[(methylsulfonyl)amino]benzamide
ChEMBL
DrugBank
ZINCZINC000000571921
PDB chain5rmd 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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PDB5rmd Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution1.92 Å
Binding residue
(original residue number in PDB)		R129 L132 F133 E136 L235 S236
Binding residue
(residue number reindexed from 1)		R121 L124 F125 E128 L215 S216
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:5rmd, PDBe:5rmd, PDBj:5rmd
PDBsum5rmd
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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