Structure of PDB 5rlh Chain B Binding Site BS01

Receptor Information
>5rlh 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 IDK2P
InChIInChI=1S/C8H5F3O3/c9-8(10,11)14-6-4-2-1-3-5(6)7(12)13/h1-4H,(H,12,13)
InChIKeyJMYSPFGUBNENSE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1ccc(c(c1)OC(F)(F)F)C(O)=O
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(=O)O)OC(F)(F)F
CACTVS 3.385OC(=O)c1ccccc1OC(F)(F)F
FormulaC8 H5 F3 O3
Name2-(trifluoromethoxy)benzoic acid
ChEMBL
DrugBank
ZINCZINC000000167135
PDB chain5rlh 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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PDB5rlh Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.379 Å
Binding residue
(original residue number in PDB)		H482 S486 Y515 T552 H554
Binding residue
(residue number reindexed from 1)		H474 S478 Y507 T544 H546
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:5rlh, PDBe:5rlh, PDBj:5rlh
PDBsum5rlh
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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