Structure of PDB 5sma Chain D Binding Site BS04

Receptor Information
>5sma 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 IDNZD
InChIInChI=1S/C12H17N3O/c1-14-7-9-15(10-8-14)12(16)13-11-5-3-2-4-6-11/h2-6H,7-10H2,1H3,(H,13,16)
InChIKeySXNAOFHNRSEHNL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.6		CN1CCN(CC1)C(=O)Nc2ccccc2
ACDLabs 12.01N1(CCN(CC1)C(Nc2ccccc2)=O)C
FormulaC12 H17 N3 O
Name4-methyl-N-phenylpiperazine-1-carboxamide
ChEMBLCHEMBL1622367
DrugBank
ZINCZINC000000236021
PDB chain5sma 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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PDB5sma PanDDA analysis group deposition
Resolution2.011 Å
Binding residue
(original residue number in PDB)		I332 Y351 L366 F367 Y368 S369 S374 D375
Binding residue
(residue number reindexed from 1)		I275 Y294 L309 F310 Y311 S312 S317 D318
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:5sma, PDBe:5sma, PDBj:5sma
PDBsum5sma
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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