Structure of PDB 6agt Chain D Binding Site BS01

Receptor Information
>6agt Chain D (length=485) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHL
EDTILNITGRIMRVSKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAECYD
KIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKEIRYRQRY
LDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLIAGGANAR
PFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTH
NPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQ
PIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIE
LPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGL
TERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDRQLDSAFCTSLEYG
LPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP
Ligand information
Ligand ID9X0
InChIInChI=1S/C17H19NO3/c19-14-10-16(21-15-9-5-4-8-13(14)15)17(20)18-11-12-6-2-1-3-7-12/h4-5,8-10,12H,1-3,6-7,11H2,(H,18,20)
InChIKeyZNVNVRHEGZKDAE-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(NCC1CCCCC1)C2=CC(=O)c3ccccc3O2
ACDLabs 12.01c13c(cccc1)C(=O)C=C(C(NCC2CCCCC2)=O)O3
OpenEye OEToolkits 2.0.6c1ccc2c(c1)C(=O)C=C(O2)C(=O)NCC3CCCCC3
FormulaC17 H19 N O3
NameN-(cyclohexylmethyl)-4-oxo-4H-1-benzopyran-2-carboxamide
ChEMBLCHEMBL549020
DrugBank
ZINC
PDB chain6agt Chain D Residue 601 [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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PDB6agt Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Resolution1.953 Å
Binding residue
(original residue number in PDB)		H338 N339 F342 G554 R559
Binding residue
(residue number reindexed from 1)		H250 N251 F254 G458 R463
Annotation score1
Binding affinityMOAD: ic50=0.004uM
Enzymatic activity
Catalytic site (original residue number in PDB) R330 E332 T337 H338 E500 N503 R559
Catalytic site (residue number reindexed from 1) R242 E244 T249 H250 E412 N415 R463
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6agt, PDBe:6agt, PDBj:6agt
PDBsum6agt
PubMed30894487
UniProtQ8IDJ8

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