Structure of PDB 5ccv Chain H Binding Site BS03

Receptor Information
>5ccv Chain H (length=767) Species: 408870 (Dengue virus 3 Philippines/H87/1956) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLGEKWKKKLNQLSRKEFDLYKKSGITEVDRTEAKEGLKRGEITHHAVSR
GSAKLQWFVERNMVIPEGRVIDLGCGRGGWSYYCAGLKKVTEVRGYTKGG
PGHEEPVPMSTYGWNIVKLMSGKDVFYLPPEKCDTLLCDISPSPTVEESR
TIRVLKMVEPWLKNNQFCIKVLNPYMPTVIEHLERLQRKHGGMLVRNPLS
RNSTHEMYWISNNIVSSVNMVSRLLLNRFTMTHRRPTIEKDVDLGAGTRH
VNAEPETPNMDVIGERIKRIKEEHSSTWHYDDENPYKTWAYHGSYEVNGV
VKLLTKPWDVVPMVTQTTPFGQQRVFKEKVDTRTPRPMPGTRKVMEITAE
WLWRTLGRNKRPRLCTREEFTKKVSARAAVEDEEFWKLVDRERELHKLGK
CGSCGARYLEFEALGFLNEDHWFSRENSYSGVEGEGLHKLGYILRDISKI
PGGAMYADDTAGWDTRITEDDLHNEEKITQDPEHRQLANAIFKLTYQNKV
VKVQRPTPKGTVMDIISRKDQRGSGQVGTYGLNTFTNMEAQLIRQMEGEG
VLSKADLENPHPLEKKITQWLETKGVERLKRMAISGDDCVVKPIDDRFAN
ALLALNDMGKVRKDIPQWQPSKGWHDWQQVPFCSHHFHELIMKDGRKLVV
PCRPQDELIGRWSLRETACLGKAYAQMWALMYFHRRDLRLASNAICSATT
EDMLTVWNRVWIEDNPWMEDKTPVTTWEDVPYLGKREDQWCGSLIGLTSR
ATWAQNILTAIQQVRSL
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 chain5ccv Chain H Residue 1003 [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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PDB5ccv Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		G81 G86 W87 T104 K105 D131 V132 D146
Binding residue
(residue number reindexed from 1)		G74 G79 W80 T97 K98 D124 V125 D139
Annotation score5
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: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:5ccv, PDBe:5ccv, PDBj:5ccv
PDBsum5ccv
PubMed26895240
UniProtP27915|POLG_DEN3P Genome polyprotein

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