Structure of PDB 6kr3 Chain A Binding Site BS02

Receptor Information
>6kr3 Chain A (length=842) Species: 11060 (dengue virus type 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLGEKWKNRLNALGKSEFQIYKKSGIQEVDRTLAKEGIKRGETDHHAVSR
GSAKLRWFVERNLVTPEGKVVDLGCGRGGWSYYCGGLKNVKEVKGLTKGG
PGHEEPIPMSTYGWNLVRLQSGVDVFFTPPEKCDTLLCDIGESSPNPTVE
AGRTLRVLNLVENWLNNNTQFCIKVLNPYMPSVIEKMEALQRKYGGALVR
NPLSRNSTHEMYWVSNASGNIVSSVNMISRMLINRFTMRHKKATYEPDVD
LGSGTRNIGIESETPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHG
SYETKQTSMVNGVVRLLTKPWDIIPMVTQMAMTDTTPFGQQRVFKEKVDT
RTQEPKEGTKKLMKITAEWLWKELGKKKTPRMCTREEFTRKVRSWKSARE
AVEDSGFWELVDKERNLHLEGKCETCVYNMMSRAIWYMWLGARFLEFEAL
GFLNEDHWFSRENSLSGVEGEGLHKLGYILRDVSKKEGGAMYADDTAGWD
TRITLEDLKNEEMVTNHMEGEHKKLAEAIFKLTYQNKVVRVQRPTPRGTV
MDIISRRDQRGSGQVVTYGLNTFTNMEAQLIRQMEGEGVFKSIQHLTVTE
EIAVKNWLVRVGRERLSRMAISGDDCVVKPLDDRFASALTALNDMGKVRK
DIQQWEPSRGWNDWTQVPFCSHHFHELIMKDGRVLVVPCRNQDELIGRAR
ISQGAGWSLRETACLGKSYAQMWSLMYFHRRDLRLAANAICSAVPSHWVP
TSRTTWTHEWMTTEDMLTVWNRVWIQENPWMEDKTPVESWEEIPYLGKRE
DQWCGSLIGLTSRATWAKNIQTAINQVRSLIGNEEYTDYMPS
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain6kr3 Chain A Residue 1014 [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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PDB6kr3 A conformation-based intra-molecular initiation factor identified in the flavivirus RNA-dependent RNA polymerase.
Resolution2.931 Å
Binding residue
(original residue number in PDB)		L70 N223
Binding residue
(residue number reindexed from 1)		L63 N216
Annotation score2
Enzymatic activity
Enzyme Commision number 3.4.21.91: flavivirin.
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0003968 RNA-dependent RNA polymerase activity
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0005524 ATP binding
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6kr3, PDBe:6kr3, PDBj:6kr3
PDBsum6kr3
PubMed32357182
UniProtQ91H74

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