Structure of PDB 4ycu Chain B Binding Site BS02

Receptor Information
>4ycu Chain B (length=499) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DPNQYYKIRSQAIHQLKVNGEDPYPHKFHVDISLTDFIQKYSHLQPGDHL
TDITLKVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSRNYKSEEEFIH
INNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLDKETR
YRQRYLDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPG
GAVAKPFITYHNELDMNLYMRIAPELYHKMLVVGGIDRVYEIGRQFRNEG
IDLTHNPEFTTCEFYMAYADYHDLMEITEKMVSGMVKHITGSYKVTYHPD
GPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRKILDDI
CVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSPLAKWH
RSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAAGDDEA
MFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFPAMKP
Ligand information
Ligand IDLYS
InChIInChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/p+1/t5-/m0/s1
InChIKeyKDXKERNSBIXSRK-YFKPBYRVSA-O
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCCC[NH3+])C(O)=O
ACDLabs 10.04O=C(O)C(N)CCCC[NH3+]
OpenEye OEToolkits 1.5.0C(CC[NH3+])C[C@@H](C(=O)O)N
CACTVS 3.341N[C@@H](CCCC[NH3+])C(O)=O
OpenEye OEToolkits 1.5.0C(CC[NH3+])CC(C(=O)O)N
FormulaC6 H15 N2 O2
NameLYSINE
ChEMBL
DrugBank
ZINC
PDB chain4ycu Chain B Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		G277 E301 E339 Y341 N497 Y499 E501 G546 W547
Binding residue
(residue number reindexed from 1)		G201 E225 E263 Y265 N421 Y423 E425 G470 W471
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R323 E325 T330 H331 E494 N497 R553
Catalytic site (residue number reindexed from 1) R247 E249 T254 H255 E418 N421 R477
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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