Structure of PDB 4ycw Chain A Binding Site BS04

Receptor Information
>4ycw Chain A (length=501) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLLKDKE
TRYRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNII
PGGAVAKPFITYHNELDMNLYMRIATELYHKMLVVGGIDRVYEIGRVFRN
EGIDLTHNPEFTSCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYH
PDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILD
DICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAK
WHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDD
EAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMK
P
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 chain4ycw Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ycw Structural Basis for Specific Inhibition of tRNA Synthetase by ATP Competitive Inhibitor
Resolution2.9 Å
Binding residue
(original residue number in PDB)
R323 E325 H331 N332 F335 E494 I495 C496 N497 G550 R553
Binding residue
(residue number reindexed from 1)
R249 E251 H257 N258 F261 E420 I421 C422 N423 G476 R479
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.68,Kd=2.1uM
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) R249 E251 T256 H257 E420 N423 R479
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:4ycw, PDBe:4ycw, PDBj:4ycw
PDBsum4ycw
PubMed
UniProtQ15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)

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