Structure of PDB 5sm0 Chain D Binding Site BS04

Receptor Information
>5sm0 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 IDLQI
InChIInChI=1S/C15H17NO2/c1-11-6-8-16(9-7-11)15(17)14-10-12-4-2-3-5-13(12)18-14/h2-5,10-11H,6-9H2,1H3
InChIKeyXNQRJSVFBWPVGG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CC1CCN(CC1)C(=O)c1cc2ccccc2o1
OpenEye OEToolkits 2.0.7CC1CCN(CC1)C(=O)c2cc3ccccc3o2
CACTVS 3.385CC1CCN(CC1)C(=O)c2oc3ccccc3c2
FormulaC15 H17 N O2
Name(1-benzofuran-2-yl)(4-methylpiperidin-1-yl)methanone
ChEMBLCHEMBL1326434
DrugBank
ZINCZINC000000620251
PDB chain5sm0 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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PDB5sm0 PanDDA analysis group deposition
Resolution2.086 Å
Binding residue
(original residue number in PDB)		N334 P355 N386 F401 Y420 F426 F506
Binding residue
(residue number reindexed from 1)		N277 P298 N327 F342 Y361 F367 F441
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:5sm0, PDBe:5sm0, PDBj:5sm0
PDBsum5sm0
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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