Structure of PDB 5rlr Chain B Binding Site BS01

Receptor Information
>5rlr 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 IDVWD
InChIInChI=1S/C9H12O3S/c1-13(11,12)7-9(10)8-5-3-2-4-6-8/h2-6,9-10H,7H2,1H3/t9-/m0/s1
InChIKeyFVZQEVNJWREWHU-VIFPVBQESA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[S](=O)(=O)C[C@H](O)c1ccccc1
OpenEye OEToolkits 2.0.7CS(=O)(=O)C[C@@H](c1ccccc1)O
CACTVS 3.385C[S](=O)(=O)C[CH](O)c1ccccc1
ACDLabs 12.01c1(C(CS(C)(=O)=O)O)ccccc1
OpenEye OEToolkits 2.0.7CS(=O)(=O)CC(c1ccccc1)O
FormulaC9 H12 O3 S
Name(1R)-2-(methylsulfonyl)-1-phenylethan-1-ol
ChEMBL
DrugBank
ZINCZINC000000393328
PDB chain5rlr 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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PDB5rlr Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.32 Å
Binding residue
(original residue number in PDB)		G285 T286 G287 H290 R442 R443 E540
Binding residue
(residue number reindexed from 1)		G280 T281 G282 H285 R434 R435 E532
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:5rlr, PDBe:5rlr, PDBj:5rlr
PDBsum5rlr
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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