Structure of PDB 5rm8 Chain A Binding Site BS01

Receptor Information
>5rm8 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 IDGQJ
InChIInChI=1S/C11H13NO5/c1-16-11(15)8-5-7(13)6-12(8)10(14)9-3-2-4-17-9/h2-4,7-8,13H,5-6H2,1H3/t7-,8+/m1/s1
InChIKeyGVYWVRYDCMRUCE-SFYZADRCSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COC(=O)[C@@H]1C[C@@H](O)CN1C(=O)c2occc2
OpenEye OEToolkits 2.0.6COC(=O)[C@@H]1C[C@H](CN1C(=O)c2ccco2)O
OpenEye OEToolkits 2.0.6COC(=O)C1CC(CN1C(=O)c2ccco2)O
CACTVS 3.385COC(=O)[CH]1C[CH](O)CN1C(=O)c2occc2
FormulaC11 H13 N O5
Namemethyl (2~{S},4~{R})-1-(furan-2-ylcarbonyl)-4-oxidanyl-pyrrolidine-2-carboxylate
ChEMBL
DrugBank
ZINCZINC000001393275
PDB chain5rm8 Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rm8 Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase.
Resolution2.143 Å
Binding residue
(original residue number in PDB)		A463 D466 K467
Binding residue
(residue number reindexed from 1)		A443 D446 K447
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:5rm8, PDBe:5rm8, PDBj:5rm8
PDBsum5rm8
PubMed34381037
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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