Structure of PDB 5ekx Chain A Binding Site BS02

Receptor Information
>5ekx Chain A (length=256) Species: 408870 (Dengue virus 3 Philippines/H87/1956) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGETTHHAVS
RGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKG
GPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTV
EESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVR
NPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVD
LGAGTR
Ligand information
Ligand ID2CQ
InChIInChI=1S/C7H9ClN2/c1-4-2-6(9)7(10)3-5(4)8/h2-3H,9-10H2,1H3
InChIKeyHOFKXNBVTNUDSH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1cc(c(cc1Cl)N)N
CACTVS 3.385Cc1cc(N)c(N)cc1Cl
ACDLabs 12.01Clc1cc(c(N)cc1C)N
FormulaC7 H9 Cl N2
Name4-chloro-5-methylbenzene-1,2-diamine
ChEMBLCHEMBL3237625
DrugBank
ZINCZINC000000153342
PDB chain5ekx Chain A Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ekx Discovery of novel dengue virus NS5 methyltransferase non-nucleoside inhibitors by fragment-based drug design.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		G107 P108 E112
Binding residue
(residue number reindexed from 1)		G101 P102 E106
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.03,IC50=9.3mM
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.
3.4.21.91: flavivirin.
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ekx, PDBe:5ekx, PDBj:5ekx
PDBsum5ekx
PubMed27750202
UniProtP27915|POLG_DEN3P Genome polyprotein

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