Structure of PDB 4yrt Chain A Binding Site BS02

Receptor Information
>4yrt Chain A (length=414) Species: 353153 (Trypanosoma cruzi strain CL Brener) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVETEPVQGCRDFPPEAMRCRRHLFDVFHATAKTFGFEEYDAPVLESEEL
YIRKAGEEITEQMFNFITKGGHRVALRPEMTPSLARLLLGKGRSLLLPAK
WYSIPQCWRYERRREHYQWNMDIVGVKSVSAEVELVCAACWAMRSLGLSS
KDVGIKVNSRKVLQTVVEQAGVTSDKFAPVCVIVDKMEKIPREEVEAQLA
VLGLEPTVVDAITTTLSLKSIDEIAQRVGEEHEAVKELRQFFEQVEAYGY
GDWVLFDASVVRGLAYYTGIVFEGFDREGKFRALCGGGRYDNLLTTYGSP
TPIPCAGFGFGDCVIVELLQEKRLLPDIPHVVDDVVIPFDESMRPHALAV
LRRLRDAGRSADIILDKKKVVQAFNYADRVGAVRAVLVAPEEWERGEVQV
KMLRGFAVPLDRLV
Ligand information
Ligand ID781
InChIInChI=1S/C13H13NO2/c1-2-13(16)14-10-6-7-11-9(8-10)4-3-5-12(11)15/h3-8,15H,2H2,1H3,(H,14,16)
InChIKeyIPFXHEAWAKCIPJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCC(=O)Nc1ccc2c(c1)cccc2O
ACDLabs 12.01O=C(Nc2cc1cccc(O)c1cc2)CC
CACTVS 3.385CCC(=O)Nc1ccc2c(O)cccc2c1
FormulaC13 H13 N O2
NameN-(5-hydroxynaphthalen-2-yl)propanamide;
N-(5-hydroxynaphthalen-2-yl)prop-2-enamide, bound form
ChEMBL
DrugBank
ZINCZINC000263620562
PDB chain4yrt Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4yrt A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.
Resolution2.05 Å
Binding residue
(original residue number in PDB)		R156 R166 E167 H168 C365 V366
Binding residue
(residue number reindexed from 1)		R109 R114 E115 H116 C313 V314
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.78,IC50=1.65mM
Enzymatic activity
Enzyme Commision number 6.1.1.21: histidine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0004821 histidine-tRNA ligase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
Biological Process
GO:0006427 histidyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yrt, PDBe:4yrt, PDBj:4yrt
PDBsum4yrt
PubMed26249349
UniProtQ4DA54

[Back to BioLiP]