Structure of PDB 5rm0 Chain B Binding Site BS01

Receptor Information
>5rm0 Chain B (length=585) 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]
VGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCN
APGCDVTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSD
NVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGI
ATVREVLSDRELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFE
KGAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTLVPQEHYVRITGLYPT
LNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIV
YTACSHAAVDALCEKALKYLPIDKCSRIIPAVECFDKFKVNSTLEQYVFC
TVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQLPAP
RTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYD
NKLKAHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRK
AVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNV
NRFNVAITRAKVGILCIMSDRDLYDKLQFTSLEIP
Ligand information
Ligand IDS7G
InChIInChI=1S/C11H14N2O/c1-8(14)13-10-6-9-4-2-3-5-11(9)12-7-10/h2-5,10,12H,6-7H2,1H3,(H,13,14)/t10-/m1/s1
InChIKeyHCEIEGOMGWEGOJ-SNVBAGLBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(=O)NC1Cc2ccccc2NC1
CACTVS 3.385CC(=O)N[C@H]1CNc2ccccc2C1
CACTVS 3.385CC(=O)N[CH]1CNc2ccccc2C1
OpenEye OEToolkits 2.0.6CC(=O)N[C@@H]1Cc2ccccc2NC1
FormulaC11 H14 N2 O
Name~{N}-[(3~{R})-1,2,3,4-tetrahydroquinolin-3-yl]ethanamide
ChEMBL
DrugBank
ZINCZINC000019274807
PDB chain5rm0 Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5rm0 Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution1.909 Å
Binding residue
(original residue number in PDB)		N9 E128 L132
Binding residue
(residue number reindexed from 1)		N8 E127 L131
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:5rm0, PDBe:5rm0, PDBj:5rm0
PDBsum5rm0
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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