Structure of PDB 8gzr Chain A Binding Site BS06

Receptor Information
>8gzr Chain A (length=880) Species: 12637 (Dengue virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GETLGEKWKKRLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAV
SRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK
GGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPT
VEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLV
RNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTYRRPTIEKDV
DLGAGTRHVNAEPETPNMDVIGERIRRIKEEHSSTWHYDDENPYKTWAYH
GSYEVKATGSASSMINGVVKLLTKPWDVVPTVTQMAMTDTTPFGQQRVFK
EKVDTRTPKPMPGTRKVMEITAGWLWRTLGRNKRPRLCTREEFTKKVRTN
AAMGAVFTEENQWDSARAAVEDEEFWKLVDRERELHKQGKCGSCVYNMMG
KREKKLGEFGKAKGSRAIWYMWLGARYLEFEALGFLNEDHWFSRENSYSG
VEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKITQQ
MDPEHRQLANAIFKLTYQNKVVKVQRPTPKGTVMDIISRKDQRGSGQVGT
YGLNTFTNMEAQLIRQMEGEGVLSKTDLENPHLLEKKITQWLETKGVERL
KRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQ
VPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLKETACLG
KAYAQMWALMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMT
TEDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPYLGKREDQWCGSLIGLTS
RATWAQNILTAIQQVRSLIGNEEFLDYMPS
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 chain8gzr Chain A Residue 1005 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8gzr Structures of dengue virus RNA replicase complexes.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S56 G81 G86 W87 K105 H110 E111 D131 V132 F133 D146
Binding residue
(residue number reindexed from 1)		S51 G76 G81 W82 K100 H105 E106 D126 V127 F128 D141
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:8gzr, PDBe:8gzr, PDBj:8gzr
PDBsum8gzr
PubMed37478848
UniProtQ5I3C1

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