Structure of PDB 5sm6 Chain D Binding Site BS04

Receptor Information
>5sm6 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 IDK1A
InChIInChI=1S/C9H11N3O2S/c1-5-8(6(2)14-11-5)4-12-9(13)15-7(3)10-12/h4H2,1-3H3
InChIKeyQMZRSGJUZDOFDN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N1(C(SC(=N1)C)=O)Cc2c(C)noc2C
OpenEye OEToolkits 2.0.6Cc1c(c(on1)C)CN2C(=O)SC(=N2)C
CACTVS 3.385Cc1onc(C)c1CN2N=C(C)SC2=O
FormulaC9 H11 N3 O2 S
Name3-[(3,5-dimethyl-1,2-oxazol-4-yl)methyl]-5-methyl-1,3,4-thiadiazol-2(3H)-one
ChEMBL
DrugBank
ZINCZINC000192455206
PDB chain5sm6 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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PDB5sm6 PanDDA analysis group deposition
Resolution2.29 Å
Binding residue
(original residue number in PDB)		S112 P412
Binding residue
(residue number reindexed from 1)		S83 P353
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:5sm6, PDBe:5sm6, PDBj:5sm6
PDBsum5sm6
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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