Structure of PDB 6kcn Chain B Binding Site BS01

Receptor Information
>6kcn Chain B (length=500) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHL
EDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFA
ECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKKDTE
IRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLI
AGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRN
EGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYN
KDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINI
IKEHKIELPPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKYH
RTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDREKGDTEA
AQLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRPA
Ligand information
Ligand IDD5F
InChIInChI=1S/C17H20O4/c1-10-3-2-4-11(5-10)6-14-8-12-7-13(18)9-15(19)16(12)17(20)21-14/h7-11,18-19H,2-6H2,1H3/t10-,11-/m0/s1
InChIKeyJSPLICPLSKXJBM-QWRGUYRKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1CCCC(C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O
OpenEye OEToolkits 2.0.7C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O
CACTVS 3.385C[CH]1CCC[CH](C1)CC2=Cc3cc(O)cc(O)c3C(=O)O2
CACTVS 3.385C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(O)cc(O)c3C(=O)O2
FormulaC17 H20 O4
Name3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one
ChEMBL
DrugBank
ZINC
PDB chain6kcn 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]
PDB6kcn Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R330 E332 H338 N339 F342 E500 L502 G554 R559
Binding residue
(residue number reindexed from 1)		R249 E251 H257 N258 F261 E418 L420 G472 R477
Annotation score1
Binding affinityMOAD: ic50=276nM
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 E418 N421 R477
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6kcn, PDBe:6kcn, PDBj:6kcn
PDBsum6kcn
PubMed32195573
UniProtW7JP72

[Back to BioLiP]