Structure of PDB 5skw Chain D Binding Site BS01

Receptor Information
>5skw 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 IDLF6
InChIInChI=1S/C9H15N3OS/c1-6-10-9(14-12-6)11-8-4-2-3-7(8)5-13/h7-8,13H,2-5H2,1H3,(H,10,11,12)/t7-,8+/m0/s1
InChIKeyQUKZXHGECCPEIZ-JGVFFNPUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1=NC(SN1)=N[C@@H]2CCC[C@H]2CO
OpenEye OEToolkits 2.0.7CC1=N/C(=N/[C@@H]2CCC[C@H]2CO)/SN1
CACTVS 3.385CC1=NC(SN1)=N[CH]2CCC[CH]2CO
OpenEye OEToolkits 2.0.7CC1=NC(=NC2CCCC2CO)SN1
ACDLabs 12.01CC1=N\C(=N\C2CCCC2CO)SN1
FormulaC9 H15 N3 O S
Name{(1R,2R)-2-[(Z)-(3-methyl-1,2,4-thiadiazol-5(2H)-ylidene)amino]cyclopentyl}methanol
ChEMBL
DrugBank
ZINCZINC000195531027
PDB chain5skw Chain D Residue 601 [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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PDB5skw PanDDA analysis group deposition
Resolution2.093 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:5skw, PDBe:5skw, PDBj:5skw
PDBsum5skw
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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