Structure of PDB 5sm1 Chain D Binding Site BS04

Receptor Information
>5sm1 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 IDWH1
InChIInChI=1S/C15H16N2O/c1-17(12-10-14-9-5-6-11-16-14)15(18)13-7-3-2-4-8-13/h2-9,11H,10,12H2,1H3
InChIKeyODNBJUNZVHSOQB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.7		CN(CCc1ccccn1)C(=O)c2ccccc2
ACDLabs 12.01n1c(cccc1)CCN(C(=O)c2ccccc2)C
FormulaC15 H16 N2 O
NameN-methyl-N-[2-(pyridin-2-yl)ethyl]benzamide
ChEMBL
DrugBank
ZINCZINC000000859193
PDB chain5sm1 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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PDB5sm1 PanDDA analysis group deposition
Resolution1.941 Å
Binding residue
(original residue number in PDB)		L321 K325 F326 A344 D345 V346
Binding residue
(residue number reindexed from 1)		L264 K268 F269 A287 D288 V289
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:5sm1, PDBe:5sm1, PDBj:5sm1
PDBsum5sm1
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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