Structure of PDB 5rmj Chain B Binding Site BS01

Receptor Information
>5rmj 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 IDJOV
InChIInChI=1S/C11H14ClNO2/c1-11(2,7-14)13-10(15)8-4-3-5-9(12)6-8/h3-6,14H,7H2,1-2H3,(H,13,15)
InChIKeyXZDXDRPMHCVWBK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)(CO)NC(=O)c1cccc(c1)Cl
CACTVS 3.385CC(C)(CO)NC(=O)c1cccc(Cl)c1
ACDLabs 12.01c1ccc(cc1C(NC(C)(CO)C)=O)Cl
FormulaC11 H14 Cl N O2
Name3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide
ChEMBL
DrugBank
ZINCZINC000000621626
PDB chain5rmj Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rmj Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F472 F499 R502 N503 E591 P593
Binding residue
(residue number reindexed from 1)		F464 F491 R494 N495 E583 P585
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:5rmj, PDBe:5rmj, PDBj:5rmj
PDBsum5rmj
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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