Structure of PDB 4ycv Chain B Binding Site BS01

Receptor Information
>4ycv Chain B (length=486) Species: 5843 (Plasmodium falciparum NF54) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVDPRLYFENRSKFIQDQKDKGINPYPHKFERTISIPEFIEKYKDLGNGE
HLEDTILNITGRIMRVSAQKLRFFDLVGDGEKIQVLANYSFHNHEKGNFA
ECYDKIRRGDIVGIVGFPGKSKKGELSIFPKETILLSACLHMLPMKYGLK
DTEIRYRQRYLDLLINESSRHTFVTRTKIINFLRNFLNERGFFEVETPMM
NLIAGGANARPFITHHNDLDLDLYLRIATELPLKMLIVGGIDKVYEIGKV
FRNEGIDNTHNPEFTSCEFYWAYADYNDLIKWSEDFFSQLVYHLFGTYKI
SYNKDGPENQPIEIDFTPPYPKVSIVEEIEKVTNTILEQPFDSNETIEKM
INIIKEHKIELPNPPTAAKLLDQLASHFIENKYNDKPFFIVEHPQIMSPL
AKYHRTKPGLTERLEMFICGKEVLNAYTELNDPFKQKECFDSAFCTSLEY
GLPPTGGLGLGIDRITMFLTNKNSIKDVILFPTMRP
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 chain4ycv 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]
PDB4ycv Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.
Resolution3.406 Å
Binding residue
(original residue number in PDB)
R330 H338 N339 F342 V501 G556 R559
Binding residue
(residue number reindexed from 1)
R252 H260 N261 F264 V423 G461 R464
Annotation score1
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 R464
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:4ycv, PDBe:4ycv, PDBj:4ycv
PDBsum4ycv
PubMed26074468
UniProtW7JP72

[Back to BioLiP]