Structure of PDB 6ka6 Chain B Binding Site BS01

Receptor Information
>6ka6 Chain B (length=504) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHL
EDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFA
ECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLK
DTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMM
NLIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKV
FRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKI
SYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKM
INIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPL
AKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDREKG
DTEAAQLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPT
MRPA
Ligand information
Ligand IDD4O
InChIInChI=1S/C17H22O4/c1-10-3-2-4-11(5-10)6-14-8-12-7-13(18)9-15(19)16(12)17(20)21-14/h7,9-11,14,18-19H,2-6,8H2,1H3/t10-,11-,14-/m0/s1
InChIKeyZGIJWPKFHHUCIH-MJVIPROJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2
OpenEye OEToolkits 2.0.7C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O)O
CACTVS 3.385C[CH]1CCC[CH](C1)C[CH]2Cc3cc(O)cc(O)c3C(=O)O2
OpenEye OEToolkits 2.0.7CC1CCCC(C1)CC2Cc3cc(cc(c3C(=O)O2)O)O
FormulaC17 H22 O4
Name(3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
ChEMBL
DrugBank
ZINC
PDB chain6ka6 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6ka6 Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
Resolution1.891 Å
Binding residue
(original residue number in PDB)
R330 E332 H338 N339 F342 E500 L502 G554 R559
Binding residue
(residue number reindexed from 1)
R252 E254 H260 N261 F264 E422 L424 G476 R481
Annotation score1
Binding affinityMOAD: ic50=221nM
Enzymatic activity
Catalytic site (original residue number in PDB) R330 E332 T337 H338 E500 N503 R559
Catalytic site (residue number reindexed from 1) R252 E254 T259 H260 E422 N425 R481
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

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Cellular Component
External links
PDB RCSB:6ka6, PDBe:6ka6, PDBj:6ka6
PDBsum6ka6
PubMed32195573
UniProtW7JP72

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