Structure of PDB 4pg3 Chain D Binding Site BS02

Receptor Information
>4pg3 Chain D (length=484) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGEHLE
DTILNITGRIMRVSASGQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFAE
CYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLTE
IRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMMNLI
AGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKVFRN
EGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKISYN
KDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKMINI
IKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPLAKY
HRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFLDSAFCTSLEYGL
PPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP
Ligand information
Ligand IDKRS
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+/m0/s1
InChIKeyWOMKDMUZNBFXKG-ZWKOPEQDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CC1CCCC(O1)CC2Cc3cc(cc(c3C(=O)O2)O)O
ACDLabs 12.01O=C3OC(CC1OC(CCC1)C)Cc2cc(O)cc(O)c23
OpenEye OEToolkits 1.9.2C[C@H]1CCC[C@@H](O1)C[C@H]2Cc3cc(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
CACTVS 3.385C[CH]1CCC[CH](C[CH]2Cc3cc(O)cc(O)c3C(=O)O2)O1
FormulaC16 H20 O5
Namecladosporin;
(3R)-3-[[(2R,6S)-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
ChEMBLCHEMBL448685
DrugBank
ZINC
PDB chain4pg3 Chain D Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pg3 Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.
Resolution2.696 Å
Binding residue
(original residue number in PDB)
R330 E332 H338 N339 F342 V501 G554 G556 R559
Binding residue
(residue number reindexed from 1)
R249 E251 H257 N258 F261 V420 G457 G459 R462
Annotation score1
Binding affinityBindingDB: IC50=120nM
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 E419 N422 R462
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
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
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:4pg3, PDBe:4pg3, PDBj:4pg3
PDBsum4pg3
PubMed24935905
UniProtQ8IDJ8

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