Structure of PDB 5sm5 Chain D Binding Site BS04

Receptor Information
>5sm5 Chain D (length=459) 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]
PTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMF
ITREEAIRHVRAWIGFDVEGCHGTNLPLQLGFSTGVNLVAVPTPLMYKGL
PWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTC
CLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNH
DLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINA
ACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCS
DKAYKIEELFYSYHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNL
NLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGIDY
VPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFD
TYNLWNTFT
Ligand information
Ligand IDS5J
InChIInChI=1S/C13H17N3O/c1-17-13-5-3-2-4-12(13)16-10-8-15(7-6-14)9-11-16/h2-5H,7-11H2,1H3
InChIKeyCMNAMTJQXKKSGP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.6		COc1ccccc1N2CCN(CC2)CC#N
FormulaC13 H17 N3 O
Name2-[4-(2-methoxyphenyl)piperazin-1-yl]ethanenitrile
ChEMBLCHEMBL231605
DrugBank
ZINCZINC000019512603
PDB chain5sm5 Chain D Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5sm5 PanDDA analysis group deposition
Resolution1.95 Å
Binding residue
(original residue number in PDB)		R310 Q313 H314 C340 P342
Binding residue
(residue number reindexed from 1)		R253 Q256 H257 C283 P285
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:0000175 3'-5'-RNA exonuclease activity
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004532 RNA exonuclease activity
GO:0008168 methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:5sm5, PDBe:5sm5, PDBj:5sm5
PDBsum5sm5
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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