Structure of PDB 5ulp Chain A Binding Site BS01

Receptor Information
>5ulp Chain A (length=262) Species: 64320 (Zika virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHA
VSRGSAKLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYT
KGGPGHEEPMLVQSYGWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSP
EVEEARTLRVLSMVGDWLEKRPGAFCIKVLCPYTSTMMETLERLQRRYGG
GLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRMDGPRRPVKYE
EDVNLGSGTRAV
Ligand information
Ligand IDKB1
InChIInChI=1S/C21H26FN7O5/c22-12-3-1-11(2-4-12)7-28(6-5-13(23)21(32)33)8-14-16(30)17(31)20(34-14)29-10-27-15-18(24)25-9-26-19(15)29/h1-4,9-10,13-14,16-17,20,30-31H,5-8,23H2,(H,32,33)(H2,24,25,26)/t13-,14+,16+,17+,20+/m0/s1
InChIKeyUBYUMSGWGXUICY-SWQDORGXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](CCN(C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)Cc4ccc(F)cc4)C(O)=O
CACTVS 3.385N[C@@H](CCN(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)Cc4ccc(F)cc4)C(O)=O
ACDLabs 12.01Nc1ncnc2n(cnc12)C3OC(C(C3O)O)CN(Cc4ccc(cc4)F)CCC(N)C(O)=O
OpenEye OEToolkits 2.0.6c1cc(ccc1CN(CCC(C(=O)O)N)CC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)F
OpenEye OEToolkits 2.0.6c1cc(ccc1CN(CC[C@@H](C(=O)O)N)C[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)F
FormulaC21 H26 F N7 O5
Name5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine
ChEMBLCHEMBL4518968
DrugBank
ZINC
PDB chain5ulp Chain A Residue 301 [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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PDB5ulp Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		S56 G81 G86 W87 T104 K105 H110 V130 D131 V132 F133 D146
Binding residue
(residue number reindexed from 1)		S52 G77 G82 W83 T100 K101 H106 V126 D127 V128 F129 D142
Annotation score3
Binding affinityMOAD: Kd=24.3uM
PDBbind-CN: -logKd/Ki=4.61,Kd=24.3uM
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
3.4.21.91: flavivirin.
3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0004482 mRNA 5'-cap (guanine-N7-)-methyltransferase activity
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ulp, PDBe:5ulp, PDBj:5ulp
PDBsum5ulp
PubMed28487506
UniProtA0A024B7W1|POLG_ZIKVF Genome polyprotein

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