Structure of PDB 5sld Chain D Binding Site BS04

Receptor Information
>5sld 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 IDLJ6
InChIInChI=1S/C11H18N2O2/c1-7(11(14)13(4)5)6-10-8(2)12-15-9(10)3/h7H,6H2,1-5H3/t7-/m1/s1
InChIKeyNIHQHFJWDDQIMY-SSDOTTSWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(c(on1)C)CC(C)C(=O)N(C)C
CACTVS 3.385C[CH](Cc1c(C)onc1C)C(=O)N(C)C
CACTVS 3.385C[C@H](Cc1c(C)onc1C)C(=O)N(C)C
ACDLabs 12.01CC(Cc1c(C)onc1C)C(=O)N(C)C
OpenEye OEToolkits 2.0.7Cc1c(c(on1)C)C[C@@H](C)C(=O)N(C)C
FormulaC11 H18 N2 O2
Name(2R)-3-(3,5-dimethyl-1,2-oxazol-4-yl)-N,N,2-trimethylpropanamide
ChEMBL
DrugBank
ZINCZINC000096416882
PDB chain5sld Chain D Residue 606 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5sld PanDDA analysis group deposition
Resolution1.581 Å
Binding residue
(original residue number in PDB)		P355 N386 F401 Y420 F426 T428
Binding residue
(residue number reindexed from 1)		P298 N327 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:5sld, PDBe:5sld, PDBj:5sld
PDBsum5sld
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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