Structure of PDB 8gzq Chain A Binding Site BS04

Receptor Information
>8gzq Chain A (length=852) Species: 12637 (Dengue virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETLGEKWKKRLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAVS
RGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKG
GPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPTV
EESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVR
NPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTYRRPTIEKDVD
LGAGTRHVNAEPETPNMDVIGERIRRIKEEHSSTWHYDDENPYKTWAYHG
SYEVKASMINGVVKLLTKPWDVVPTVTQMAMTDTTPFGQQRVFKEKVDTR
TPKPMPGTRKVMEITAGWLWRTLGRNKRPRLCTREEFTKKVRTNQWDSAR
AAVEDEEFWKLVDRERELHKQGKCGSCVYNMMRAIWYMWLGARYLEFEAL
GFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKIPGGAMYADDTAGWD
TRITEDDLHNEEKITQQMDPEHRQLANAIFKLTYQNKVVKVQRPTPKGTV
MDIISRKDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEGVLSKTDLENPHL
LEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFANALLALNDMGKVR
KDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVVPCRPQDELIGRA
RISQGAGWSLKETACLGKAYAQMWALMYFHRRDLRLASNAICSAVPVHWV
PTSRTTWSIHAHHQWMTTEDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPY
LGKREDQWCGSLIGLTSRATWAQNILTAIQQVRSLIGNEEFLDYMPSMKR
FR
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain8gzq Chain S Residue 201 [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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PDB8gzq Structures of dengue virus RNA replicase complexes.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		N18 L20 F25 S151 P152 S213
Binding residue
(residue number reindexed from 1)		N12 L14 F19 S145 P146 S207
Annotation score3
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:8gzq, PDBe:8gzq, PDBj:8gzq
PDBsum8gzq
PubMed37478848
UniProtQ5I3C1

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