Structure of PDB 5sme Chain D Binding Site BS04

Receptor Information
>5sme Chain D (length=461) 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
DKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLS
NLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGI
DYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQ
FDTYNLWNTFT
Ligand information
Ligand IDI8D
InChIInChI=1S/C11H12ClNOS/c12-10-3-1-9(2-4-10)11(14)13-5-7-15-8-6-13/h1-4H,5-8H2
InChIKeyPIZZAODWSORPSH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1C(=O)N2CCSCC2)Cl
CACTVS 3.385Clc1ccc(cc1)C(=O)N2CCSCC2
ACDLabs 12.01O=C(c1ccc(Cl)cc1)N1CCSCC1
FormulaC11 H12 Cl N O S
Name(4-chlorophenyl)(thiomorpholin-4-yl)methanone
ChEMBLCHEMBL1301837
DrugBank
ZINCZINC000000140258
PDB chain5sme 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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PDB5sme PanDDA analysis group deposition
Resolution1.91 Å
Binding residue
(original residue number in PDB)		I42 M57 M58 T193 K196
Binding residue
(residue number reindexed from 1)		I19 M34 M35 T136 K139
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:5sme, PDBe:5sme, PDBj:5sme
PDBsum5sme
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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