Structure of PDB 6ilh Chain B Binding Site BS01

Receptor Information
>6ilh Chain B (length=504) 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
FRNEGIDLTHNPEFTTCEFYMAYADYHDHMEITEKMVSGMVKHITGSYKV
TYHPDGPEGQAYDVDFTPPFRRINMVEELEKALGMKLPETNLFETEETRK
ILDDICVAKAVECPPPRTTARLLDKLVGEFLEVTCINPTFICDHPQIMSP
LAKWHRSKEGLTERFELFVMKKEICNAYTELNDPMRQRQLFEEQAKAKAA
GDDEAMFIDENFCTALEYGLPPTAGWGMGIDRVAMFLTDSNNIKEVLLFP
AMKP
Ligand information
Ligand IDKAA
InChIInChI=1S/C16H26N8O7S/c17-4-2-1-3-8(18)15(27)23-32(28,29)30-5-9-11(25)12(26)16(31-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,16,25-26H,1-5,17-18H2,(H,23,27)(H2,19,20,21)/t8-,9+,11+,12+,16+/m0/s1
InChIKeyNARKTLKJPPMFJF-LEJQEAHTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COS(=O)(=O)NC(=O)[C@H](CCCCN)N)O)O)N
CACTVS 3.341NCCCC[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.341NCCCC[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)CCCCN
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COS(=O)(=O)NC(=O)C(CCCCN)N)O)O)N
FormulaC16 H26 N8 O7 S
Name5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE;
5'-O-[N-(L-LYSYL)SULFAMOYL]ADENOSINE
ChEMBLCHEMBL1163083
DrugBank
ZINCZINC000040956727
PDB chain6ilh 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]
PDB6ilh Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex.
Resolution2.501 Å
Binding residue
(original residue number in PDB)		E301 R323 H331 N332 F335 E339 Y341 E494 N497 Y499 E501 G546 G548 G550 R553
Binding residue
(residue number reindexed from 1)		E230 R252 H260 N261 F264 E268 Y270 E423 N426 Y428 E430 G475 G477 G479 R482
Annotation score2
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ilh, PDBe:6ilh, PDBj:6ilh
PDBsum6ilh
PubMed30733335
UniProtQ15046|SYK_HUMAN Lysine--tRNA ligase (Gene Name=KARS1)

[Back to BioLiP]