Structure of PDB 6kr3 Chain A Binding Site BS01

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 1013 [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)		S56 G81 G86 W87 T104 K105 H110 E111 V130 D131 V132 F133 D146
Binding residue
(residue number reindexed from 1)		S49 G74 G79 W80 T97 K98 H103 E104 V123 D124 V125 F126 D139
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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