Structure of PDB 7xd9 Chain M Binding Site BS07

Receptor Information
>7xd9 Chain M (length=624) Species: 11060 (dengue virus type 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IESETPNLDIIGKRIEKIKQEHETSWHYDQDHPYKTWAYHGSYETKQTGS
ASSMVNGVVRLLTKPWDIIPMVTQMAMTDTTPFGQQRVFKEKVDTRTQEP
KEGTKKLMKITAEWLWKELGKKKTPRMCTREEFTRKVRSNAALGAIFTDE
NKWKSAREAVEDSGFWELVDKERNLHLEGKCETCVYNMMGKREKKLGEFG
KAKGSRAIWYMWLGARFLEFEALGFLNEDHWFSRENSLSGVEGEGLHKLG
YILRDVSKKEGGAMYADDTAGWDTRITLEDLKNEEMVTNHMEGEHKKLAE
AIFKLTYQNKVVRVQRPTPRGTVMDIISRRDQRGSGQVVTYGLNTFTNME
AQLIRQMEGEGVFKSIQHLTVTEEIAVKNWLVRVGRERLSRMAISGDDCV
VKPLDDRFASALTALNDMGKVRKDIQQWEPSRGWNDWTQVPFCSHHFHEL
IMKDGRVLVVPCRNQDELIGRARISQGAGWSLRETACLGKSYAQMWSLMY
FHRRDLRLAANAICSAVPSHWVPTSRTTWSIHATHEWMTTEDMLTVWNRV
WIQENPWMEDKTPVESWEEIPYLGKREDQWCGSLIGLTSRATWAKNIQTA
INQVRSLIGNEEYTDYMPSMKRFR
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain7xd9 Chain M Residue 1006 [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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PDB7xd9 Structural basis of transition from initiation to elongation in de novo viral RNA-dependent RNA polymerases.
Resolution2.58 Å
Binding residue
(original residue number in PDB)		R472 T535 G537 W538 D539 S601 D663 K689
Binding residue
(residue number reindexed from 1)		R206 T269 G271 W272 D273 S335 D397 K423
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:0005524 ATP binding
Biological Process
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7xd9, PDBe:7xd9, PDBj:7xd9
PDBsum7xd9
PubMed36577062
UniProtQ91H74

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