Structure of PDB 4pg3 Chain B Binding Site BS01

Receptor Information
>4pg3 Chain B (length=486) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLE
DTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAE
CYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLKD
TEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMN
LIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVF
RNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKIS
YNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMI
NIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLA
KYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFLDSAFCTSLEY
GLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain4pg3 Chain B Residue 601 [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]
PDB4pg3 Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.
Resolution2.696 Å
Binding residue
(original residue number in PDB)		E308 E346 Y348 N503 Y505 E507 G552
Binding residue
(residue number reindexed from 1)		E229 E267 Y269 N424 Y426 E428 G457
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R330 E332 T337 H338 E500 N503 R559
Catalytic site (residue number reindexed from 1) R251 E253 T258 H259 E421 N424 R464
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pg3, PDBe:4pg3, PDBj:4pg3
PDBsum4pg3
PubMed24935905
UniProtQ8IDJ8

[Back to BioLiP]