Structure of PDB 8gzr Chain A Binding Site BS07
Receptor Information
>8gzr Chain A (length=880) Species:
12637
(Dengue virus) [
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GETLGEKWKKRLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAV
SRGSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTK
GGPGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDIGESSPSPT
VEESRTIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLV
RNPLSRNSTHEMYWISNGTGNIVSSVNMVSRLLLNRFTMTYRRPTIEKDV
DLGAGTRHVNAEPETPNMDVIGERIRRIKEEHSSTWHYDDENPYKTWAYH
GSYEVKATGSASSMINGVVKLLTKPWDVVPTVTQMAMTDTTPFGQQRVFK
EKVDTRTPKPMPGTRKVMEITAGWLWRTLGRNKRPRLCTREEFTKKVRTN
AAMGAVFTEENQWDSARAAVEDEEFWKLVDRERELHKQGKCGSCVYNMMG
KREKKLGEFGKAKGSRAIWYMWLGARYLEFEALGFLNEDHWFSRENSYSG
VEGEGLHKLGYILRDISKIPGGAMYADDTAGWDTRITEDDLHNEEKITQQ
MDPEHRQLANAIFKLTYQNKVVKVQRPTPKGTVMDIISRKDQRGSGQVGT
YGLNTFTNMEAQLIRQMEGEGVLSKTDLENPHLLEKKITQWLETKGVERL
KRMAISGDDCVVKPIDDRFANALLALNDMGKVRKDIPQWQPSKGWHDWQQ
VPFCSHHFHELIMKDGRKLVVPCRPQDELIGRARISQGAGWSLKETACLG
KAYAQMWALMYFHRRDLRLASNAICSAVPVHWVPTSRTTWSIHAHHQWMT
TEDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPYLGKREDQWCGSLIGLTS
RATWAQNILTAIQQVRSLIGNEEFLDYMPS
Ligand information
Ligand ID
CDP
InChI
InChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey
ZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
Software
SMILES
OpenEye OEToolkits 1.5.0
C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341
NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04
O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0
C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341
NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
Formula
C9 H15 N3 O11 P2
Name
CYTIDINE-5'-DIPHOSPHATE
ChEMBL
CHEMBL425252
DrugBank
DB04555
ZINC
ZINC000008215624
PDB chain
8gzr Chain A Residue 1006 [
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Receptor-Ligand Complex Structure
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PDB
8gzr
Structures of dengue virus RNA replicase complexes.
Resolution
2.8 Å
Binding residue
(original residue number in PDB)
R471 D533 G536 W537 D538 S600 D663
Binding residue
(residue number reindexed from 1)
R466 D528 G531 W532 D533 S595 D658
Annotation score
2
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
PDBsum
8gzr
PubMed
37478848
UniProt
Q5I3C1
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