Structure of PDB 2yol Chain A Binding Site BS01

Receptor Information
>2yol Chain A (length=212) Species: 11082 (West Nile virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMTDMWIERTADITWESDAEITGSSERVDVRLDDDGNFQLMNDPGVLWD
TSPKEYKKGDTTTGVYRIMTRGLLGSYQAGAGVMVEGVFHTLWHTTKGAA
LMSGEGRLDPYWGSVKEDRLCYGGPWKLQHKWNGHDEVQMIVVEPGKNVK
NVQTKPGVFKTPEGEIGAVTLDYPTGTSGSPIVDKNGDVIGLYGNGVIMP
NGSYISAIVQGE
Ligand information
Ligand IDEBN
InChIInChI=1S/C28H46Cl2N8O3/c29-21-12-9-19(15-22(21)30)16-25(39)37-24(6-2-4-14-32)27(41)38-23(5-1-3-13-31)26(40)35-17-18-7-10-20(11-8-18)36-28(33)34/h9,12,15,18,20,23-24H,1-8,10-11,13-14,16-17,31-32H2,(H,35,40)(H,37,39)(H,38,41)(H4,33,34,36)/t18-,20-,23-,24-/m0/s1
InChIKeyOWKCLMWSCHVRNJ-BTDFZRAWSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NCCCC[C@H](NC(=O)[C@H](CCCCN)NC(=O)Cc1ccc(Cl)c(Cl)c1)C(=O)NC[C@H]2CC[C@@H](CC2)NC(N)=N
CACTVS 3.370NCCCC[CH](NC(=O)[CH](CCCCN)NC(=O)Cc1ccc(Cl)c(Cl)c1)C(=O)NC[CH]2CC[CH](CC2)NC(N)=N
OpenEye OEToolkits 1.7.6c1cc(c(cc1CC(=O)NC(CCCCN)C(=O)NC(CCCCN)C(=O)NCC2CCC(CC2)NC(=N)N)Cl)Cl
OpenEye OEToolkits 1.7.6[H]/N=C(\N)/NC1CCC(CC1)CNC(=O)[C@H](CCCCN)NC(=O)[C@H](CCCCN)NC(=O)Cc2ccc(c(c2)Cl)Cl
ACDLabs 12.01Clc1ccc(cc1Cl)CC(=O)NC(C(=O)NC(C(=O)NCC2CCC(NC(=[N@H])N)CC2)CCCCN)CCCCN
FormulaC28 H46 Cl2 N8 O3
Name(S)-6-amino-N-((S)-6-amino-1-(((1r,4S)-4-guanidinocyclohexyl)methylamino)-1-oxohexan-2-yl)-2-(2-(3,4-dichlorophenyl)acetamido)hexanamide;
3,4-dichlorophenylacetyl-Lys-Lys-GCMA
ChEMBLCHEMBL3344321
DrugBank
ZINC
PDB chain2yol Chain A Residue 2170 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yol Development and Characterization of New Peptidomimetic Inhibitors of the West Nile Virus Ns2B-Ns3 Protease.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		G83 F85 H1051 D1075 D1129 Y1130 T1132 G1151 N1152 G1153 I1155 Y1161
Binding residue
(residue number reindexed from 1)		G37 F39 H94 D118 D172 Y173 T175 G194 N195 G196 I198 Y204
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.89,Ki=0.13uM
BindingDB: Ki=130nM
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:0004252 serine-type endopeptidase activity
GO:0005524 ATP binding
Cellular Component
GO:0044423 virion component

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:2yol, PDBe:2yol, PDBj:2yol
PDBsum2yol
PubMed23307694
UniProtP06935|POLG_WNV Genome polyprotein

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