Structure of PDB 5rml Chain A Binding Site BS01

Receptor Information
>5rml 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 IDVXD
InChIInChI=1S/C9H11ClN2O/c1-6-7(10)3-2-4-8(6)12-9(13)5-11/h2-4H,5,11H2,1H3,(H,12,13)
InChIKeyFPQHYOUXKZRHSA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1c(Cl)cccc1NC(=O)CN
OpenEye OEToolkits 2.0.7Cc1c(cccc1Cl)NC(=O)CN
ACDLabs 12.01N(C(=O)CN)c1cccc(c1C)Cl
FormulaC9 H11 Cl N2 O
NameN-(3-chloro-2-methylphenyl)glycinamide
ChEMBL
DrugBank
ZINCZINC000003399182
PDB chain5rml Chain A 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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PDB5rml Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.43 Å
Binding residue
(original residue number in PDB)		E142 F145 K146 Y180 T410 L411
Binding residue
(residue number reindexed from 1)		E134 F137 K138 Y172 T390 L391
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:5rml, PDBe:5rml, PDBj:5rml
PDBsum5rml
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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