Structure of PDB 4ycu Chain A Binding Site BS01

Receptor Information
>4ycu Chain A (length=505) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLK
DKETRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMM
NIIPGGAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQ
FRNEGIDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKV
TYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRK
ILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSP
LAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAA
GDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFP
AMKPE
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 chain4ycu Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ycu Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		E325 H331 N332 F335 N497 G550 R553
Binding residue
(residue number reindexed from 1)		E254 H260 N261 F264 N426 G479 R482
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.48,Kd=3.3uM
BindingDB: IC50=>20000nM
Enzymatic activity
Catalytic site (original residue number in PDB) R323 E325 T330 H331 E494 N497 R553
Catalytic site (residue number reindexed from 1) R252 E254 T259 H260 E423 N426 R482
Enzyme Commision number 2.7.7.-
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:4ycu, PDBe:4ycu, PDBj:4ycu
PDBsum4ycu
PubMed26074468
UniProtQ15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)

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