Structure of PDB 5sm4 Chain D Binding Site BS04

Receptor Information
>5sm4 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 IDAWD
InChIInChI=1S/C12H16FN3O/c1-15-6-8-16(9-7-15)12(17)14-11-4-2-10(13)3-5-11/h2-5H,6-9H2,1H3,(H,14,17)
InChIKeyMDBPFVSVLGYVCQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCN(CC1)C(=O)Nc2ccc(F)cc2
OpenEye OEToolkits 2.0.6CN1CCN(CC1)C(=O)Nc2ccc(cc2)F
FormulaC12 H16 F N3 O
Name~{N}-(4-fluorophenyl)-4-methyl-piperazine-1-carboxamide
ChEMBLCHEMBL4514548
DrugBank
ZINCZINC000000386890
PDB chain5sm4 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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PDB5sm4 PanDDA analysis group deposition
Resolution2.16 Å
Binding residue
(original residue number in PDB)		H330 Y351 L366 F367 S369 S374 D375 F377
Binding residue
(residue number reindexed from 1)		H273 Y294 L309 F310 S312 S317 D318 F320
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:5sm4, PDBe:5sm4, PDBj:5sm4
PDBsum5sm4
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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