Structure of PDB 5lc0 Chain B Binding Site BS02

Receptor Information
>5lc0 Chain B (length=190) Species: 64320 (Zika virus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLETTDGVYRVMT
RGLLGSTQVGVGVMQEGVFHTMWHVTKGSALRSGEGRLDPYWGDVKQDLV
SYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKTKDGDIGAVA
LDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQ
Ligand information
Ligand ID6T8
InChIInChI=1S/C25H35BN6O5/c27-14-18-10-8-17(9-11-18)13-21(31-23(34)19-5-2-1-3-6-19)24(35)32-22(7-4-12-30-25(28)29)26-36-15-20(33)16-37-26/h1-3,5-6,8-11,20-22,33H,4,7,12-16,27H2,(H,31,34)(H,32,35)(H4,28,29,30)/t21-,22-/m0/s1
InChIKeyDYKCMHQIYUDANF-VXKWHMMOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCc1ccc(C[C@H](NC(=O)c2ccccc2)C(=O)N[C@@H](CCCNC(N)=N)B3OCC(O)CO3)cc1
OpenEye OEToolkits 2.0.5B1(OCC(CO1)O)C(CCCNC(=N)N)NC(=O)C(Cc2ccc(cc2)CN)NC(=O)c3ccccc3
OpenEye OEToolkits 2.0.5[H]/N=C(/N)\NCCC[C@@H](B1OCC(CO1)O)NC(=O)[C@H](Cc2ccc(cc2)CN)NC(=O)c3ccccc3
CACTVS 3.385NCc1ccc(C[CH](NC(=O)c2ccccc2)C(=O)N[CH](CCCNC(N)=N)B3OCC(O)CO3)cc1
FormulaC25 H35 B N6 O5
NameN-((S)-3-(4-(aminomethyl)phenyl)-1-(((R)-4-guanidino-1-(5-hydroxy-1,3,2-dioxaborinan-2-yl)butyl)amino)-1-oxopropan-2-yl)benzamide
ChEMBL
DrugBank
ZINCZINC000584904967
PDB chain5lc0 Chain B Residue 1201 [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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PDB5lc0 Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		S81 G82 D83 V1036 H1051 Y1130 A1132 G1133 S1135 G1151 N1152 V1154 Y1161
Binding residue
(residue number reindexed from 1)		S34 G35 D36 V59 H74 Y153 A155 G156 S158 G174 N175 V177 Y184
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.70,IC50=0.20uM
Enzymatic activity
Enzyme Commision number 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:5lc0, PDBe:5lc0, PDBj:5lc0
PDBsum5lc0
PubMed27386922
UniProtA0A140DLX4

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