Structure of PDB 3e90 Chain D Binding Site BS02

Receptor Information
>3e90 Chain D (length=167) Species: 11082 (West Nile virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GGVLWYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAA
LMSGEGRLDPYWGSVKEDRLCYGGPWKLQHKWNGQDEVQMIVVEPGKNVK
NVRTKPGVFKTPEGEIGAVTLDFPTGTSGSPIVDKNGDVIGLYGNGVIMP
NGSYISAIVQGKRMDEP
Ligand information
Ligand IDNKK
InChIInChI=1S/C29H44N8O4/c30-15-5-3-11-24(27(40)35-23(19-38)10-7-17-34-29(32)33)37-28(41)25(12-4-6-16-31)36-26(39)22-14-13-20-8-1-2-9-21(20)18-22/h1-2,8-9,13-14,18-19,23-25H,3-7,10-12,15-17,30-31H2,(H,35,40)(H,36,39)(H,37,41)(H4,32,33,34)/t23-,24-,25-/m0/s1
InChIKeyVYVVOKKLVHYYQD-SDHOMARFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NCCCC[CH](NC(=O)[CH](CCCCN)NC(=O)c1ccc2ccccc2c1)C(=O)N[CH](CCCNC(N)=N)C=O
OpenEye OEToolkits 1.5.0[H]N=C(N)NCCCC(C=O)NC(=O)C(CCCCN)NC(=O)C(CCCCN)NC(=O)c1ccc2ccccc2c1
ACDLabs 10.04O=CC(NC(=O)C(NC(=O)C(NC(=O)c2ccc1c(cccc1)c2)CCCCN)CCCCN)CCCNC(=[N@H])N
OpenEye OEToolkits 1.5.0[H]/N=C(\N)/NCCC[C@@H](C=O)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)c1ccc2ccccc2c1
CACTVS 3.341NCCCC[C@H](NC(=O)[C@H](CCCCN)NC(=O)c1ccc2ccccc2c1)C(=O)N[C@@H](CCCNC(N)=N)C=O
FormulaC29 H44 N8 O4
NameN~2~-(naphthalen-2-ylcarbonyl)-L-lysyl-N-[(1S)-4-carbamimidamido-1-formylbutyl]-L-lysinamide
ChEMBLCHEMBL521985
DrugBank
ZINCZINC000042890354
PDB chain3e90 Chain D Residue 195 [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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PDB3e90 Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation
Resolution2.45 Å
Binding residue
(original residue number in PDB)		H51 D75 F130 S135 G151 N152 G153 Y161
Binding residue
(residue number reindexed from 1)		H44 D68 F123 S128 G144 N145 G146 Y154
Annotation score1
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:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0005524 ATP binding

View graph for
Molecular Function
External links
PDB RCSB:3e90, PDBe:3e90, PDBj:3e90
PDBsum3e90
PubMed19059417
UniProtP06935|POLG_WNV Genome polyprotein

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