Structure of PDB 5zh4 Chain A Binding Site BS02

Receptor Information
>5zh4 Chain A (length=472) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGE
HLEDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGN
FAECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKTE
IRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLI
AGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRN
EGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYN
PIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINIIKEHKIE
LPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYHRTKPGL
TERLEMFICGKEVLNAYTELNDPFKQKEAFCTSLEYGLPPTGGLGLGIDR
ITMFLTNKNSIKDVILFPTMRP
Ligand information
Ligand ID9CC
InChIInChI=1S/C16H20O5/c1-9-3-2-4-12(20-9)8-13-6-10-5-11(17)7-14(18)15(10)16(19)21-13/h5,7,9,12-13,17-18H,2-4,6,8H2,1H3/t9-,12+,13-/m1/s1
InChIKeyWOMKDMUZNBFXKG-JIMOISOXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1CCCC(O1)CC2Cc3cc(cc(c3C(=O)O2)O)O
CACTVS 3.385C[C@@H]1CCC[C@@H](C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2)O1
OpenEye OEToolkits 2.0.6C[C@@H]1CCC[C@H](O1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O)O
CACTVS 3.385C[CH]1CCC[CH](C[CH]2Cc3cc(O)cc(O)c3C(=O)O2)O1
ACDLabs 12.01c2(cc(cc3CC(CC1CCCC(C)O1)OC(c23)=O)O)O
FormulaC16 H20 O5
Name(3R)-6,8-dihydroxy-3-{[(2S,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one
ChEMBLCHEMBL578530
DrugBank
ZINC
PDB chain5zh4 Chain A Residue 602 [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)		E332 H338 N339 F342 V501 L502 R559
Binding residue
(residue number reindexed from 1)		E251 H257 N258 F261 V413 L414 R450
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.14,IC50=7.25uM
Enzymatic activity
Catalytic site (original residue number in PDB) R330 E332 T337 H338 E500 N503 R559
Catalytic site (residue number reindexed from 1) R249 E251 T256 H257 E412 N415 R450
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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