Structure of PDB 5rlf Chain A Binding Site BS01

Receptor Information
>5rlf 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 IDNY7
InChIInChI=1S/C10H14N2O2/c1-7-3-4-9(14-2)8(5-7)12-10(13)6-11/h3-5H,6,11H2,1-2H3,(H,12,13)
InChIKeySRFLDWOWAGQZAD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1ccc(c(c1)NC(=O)CN)OC
ACDLabs 12.01N(c1cc(ccc1OC)C)C(CN)=O
CACTVS 3.385COc1ccc(C)cc1NC(=O)CN
FormulaC10 H14 N2 O2
NameN-(2-methoxy-5-methylphenyl)glycinamide
ChEMBL
DrugBank
ZINCZINC000004201706
PDB chain5rlf 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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PDB5rlf Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.235 Å
Binding residue
(original residue number in PDB)		L585 Q586 F587
Binding residue
(residue number reindexed from 1)		L565 Q566 F567
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:5rlf, PDBe:5rlf, PDBj:5rlf
PDBsum5rlf
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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