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Structure of PDB 6kcn Chain D Binding Site BS01

Receptor Information >6kcn Chain D (length=502) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] VDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEH LEDTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNF AECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYKD TEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMN LIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVF RNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKIS YNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMI NIIKEHKIELPPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAK YHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFKLQQKDREKGDT EAAQLDSAFCTSLEYGLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMR PA

Ligand information Ligand ID D5F InChI InChI=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 InChIKey JSPLICPLSKXJBM-QWRGUYRKSA-N SMILES Software SMILES OpenEye OEToolkits 2.0.7 CC1CCCC(C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O OpenEye OEToolkits 2.0.7 C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O CACTVS 3.385 C[CH]1CCC[CH](C1)CC2=Cc3cc(O)cc(O)c3C(=O)O2 CACTVS 3.385 C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(O)cc(O)c3C(=O)O2 Formula C17 H20 O4 Name 3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one ChEMBL DrugBank ZINC PDB chain 6kcn Chain D Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure 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] PDB 6kcn Atomic Resolution Analyses of Isocoumarin Derivatives for Inhibition of Lysyl-tRNA Synthetase. Resolution 2.2 Å Binding residue (original residue number in PDB) R330 E332 H338 N339 F342 L502 G554 L555 R559 Binding residue (residue number reindexed from 1) R251 E253 H259 N260 F263 L422 G474 L475 R479 Annotation score 1 Binding affinity MOAD: 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) R251 E253 T258 H259 E420 N423 R479 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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