Structure of PDB 5zh4 Chain B Binding Site BS01

Receptor Information
>5zh4 Chain B (length=476) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGEHL
EDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFA
ECYDKIRRGDIVGIVGFPGKSLSIFPKETILLSACLHMLPEIRYRQRYLD
LLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLIAGGANARPF
ITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRNEGIDNTHNP
EFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYNKDGPENQPI
EIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIELP
NPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGLTE
RLEMFICGKEVLNAYTELNDPFKQKECFQLDSAFCTSLEYGLPPTGGLGL
GIDRITMFLTNKNSIKDVILFPTMRP
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 chain5zh4 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

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PDB5zh4 Specific Stereoisomeric Conformations Determine the Drug Potency of Cladosporin Scaffold against Malarial Parasite
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G284 E308 E346 Y348 N503 Y505 E507 G552
Binding residue
(residue number reindexed from 1)		G194 E218 E256 Y258 N413 Y415 E417 G447
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) R240 E242 T247 H248 E410 N413 R454
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
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
GO:0016874 ligase activity
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zh4, PDBe:5zh4, PDBj:5zh4
PDBsum5zh4
PubMed29779382
UniProtW7JP72

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