Structure of PDB 4hdh Chain A Binding Site BS01

Receptor Information
>4hdh Chain A (length=613) Species: 11072 (Japanese encephalitis virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNQEKIKKRIQKLKEEFATTWHKDPEHPYRTWTYHGSYEVKATGLVNGVV
KLMSKPWDAIANVTTMAMTDTTPFGQQRVFKEKVDTKAPEPPAGVREVLN
ETTNWLWAHLSREKRPRLCTKEEFIKKVNSNAALGAVFAEQNQWSTAREA
VNDPRFWEMVDEERENHLRGECHTCIYNMMGKREKKPGEFGKAKGSRAIW
FMWLGARYLEFEALGFLNEDHWLSRENSGGGVEGSGVQKLGYILRDIAGK
QGGKMYADDTAGWDTRITRTDLENEAKVLELLDGEHRMLARAIIELTYRH
KVVKVMRPAAEGKTVMDVISREDQRGSGQVVTYALNTFTNIAVQLVRLME
AEGVIGPQHLEQLPRKNKIAVRTWLFENGEERVTRMAISGDDCVVKPLDD
RFATALHFLNAMSKVRKDIQEWKPSHGWHDWQQVPFCSNHFQEIVMKDGR
SIVVPCRGQDELIGRARISPGAGWNVKDTACLAKAYAQMWLLLYFHRRDL
RLMANAICSAVPVDWVPTGRTSWSIHSKGEWMTTEDMLQVWNRVWIEENE
WMMDKTPIASWTDVPYVGKREDIWCGSLIGTRSRATWAENIYAAINQVRA
VIGKENYVDYMTS
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(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)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4hdh Chain A Residue 1001 [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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PDB4hdh RNA-dependent RNA polymerase of Japanese encephalitis virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state.
Resolution2.28 Å
Binding residue
(original residue number in PDB)		K463 R474 S666 G667 D668 C714 S715 R734 R742 S799 W800 S801
Binding residue
(residue number reindexed from 1)		K186 R197 S389 G390 D391 C437 S438 R457 R465 S522 W523 S524
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:0005524 ATP binding
Biological Process
GO:0039694 viral RNA genome replication

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Molecular Function
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Biological Process
External links
PDB RCSB:4hdh, PDBe:4hdh, PDBj:4hdh
PDBsum4hdh
PubMed24293643
UniProtP27395|POLG_JAEV1 Genome polyprotein

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