Structure of PDB 5sm2 Chain D Binding Site BS04

Receptor Information
>5sm2 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 IDLQ3
InChIInChI=1S/C6H5F2NO2/c7-6(8)11-4-1-2-5(10)9-3-4/h1-4,6H/t4-/m0/s1
InChIKeyLTVXNUWMTTYHRL-BYPYZUCNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385FC(F)O[C@H]1C=CC(=O)N=C1
ACDLabs 12.01O=C1C=CC(OC(F)F)C=N1
OpenEye OEToolkits 2.0.7C1=CC(=O)N=CC1OC(F)F
CACTVS 3.385FC(F)O[CH]1C=CC(=O)N=C1
FormulaC6 H5 F2 N O2
Name(5S)-5-(difluoromethoxy)pyridin-2(5H)-one
ChEMBL
DrugBank
ZINC
PDB chain5sm2 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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PDB5sm2 PanDDA analysis group deposition
Resolution1.781 Å
Binding residue
(original residue number in PDB)		P355 F401 Y420 F426 T428
Binding residue
(residue number reindexed from 1)		P298 F342 Y361 F367 T369
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:5sm2, PDBe:5sm2, PDBj:5sm2
PDBsum5sm2
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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