Structure of PDB 6ykq Chain A Binding Site BS01

Receptor Information
>6ykq Chain A (length=847) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEHYQPAAIEPAAQKKWDDARISNVSEDASKPKYYCLSMFPYPSGKLHM
GHVRNYTIGDVLSRFKLLNGFNVMQPMGWDAFGMPAENAAMKNNVAPAAW
TYDNIEYMKTQLKSLGFAVDWEREVATCKPEYYRWEQWLFTKLFEKGIVY
RKNGTVNWDPVDQTVLANEQVIDGRGWRSGALIEKREIPMYYFKITDYAE
ELLNDLDKLEHWPEQVKTMQRNWIGKSRGMTVRFAVSDDSKQGLEGDYAK
FLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKAGSVA
EADMATMEKKGVPTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAH
DERDFEFAAKYNLPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLD
GLDFQTAFDAVAAKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCE
KCGNVPVPADQLPVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRE
TDTMDTFIESSWYFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAIL
HLLYARFFTKLMRDEGLVNVDEPFERLLTQGMVVCETYYRENDKGGKDWI
NPADVELTPVSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADT
ARLFMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFA
GNQDGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDK
TDTGSEQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPT
VDEAALVKSEIEVMVQVNGKLRGKADLEAAALANIIVVPGRLVNIVV
Ligand information
Ligand IDOVW
InChIInChI=1S/C25H47N5O7S/c1-4-5-6-7-8-9-12-20-15-30(29-27-20)13-10-11-19-16-36-22(24(32)23(19)31)17-37-38(34,35)28-25(33)21(26)14-18(2)3/h15,18-19,21-24,31-32H,4-14,16-17,26H2,1-3H3,(H,28,33)/t19-,21+,22-,23+,24-/m1/s1
InChIKeyKJHVCACMAXYEPW-MENZVKOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCCc1cn(nn1)CCCC2COC(C(C2O)O)COS(=O)(=O)NC(=O)C(CC(C)C)N
CACTVS 3.385CCCCCCCCc1cn(CCC[CH]2CO[CH](CO[S](=O)(=O)NC(=O)[CH](N)CC(C)C)[CH](O)[CH]2O)nn1
CACTVS 3.385CCCCCCCCc1cn(CCC[C@@H]2CO[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)CC(C)C)[C@@H](O)[C@H]2O)nn1
OpenEye OEToolkits 2.0.7CCCCCCCCc1cn(nn1)CCC[C@@H]2CO[C@@H]([C@H]([C@H]2O)O)COS(=O)(=O)NC(=O)[C@H](CC(C)C)N
FormulaC25 H47 N5 O7 S
Name[(2~{R},3~{S},4~{S},5~{R})-5-[3-(4-octyl-1,2,3-triazol-1-yl)propyl]-3,4-bis(oxidanyl)oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate
ChEMBLCHEMBL4867227
DrugBank
ZINC
PDB chain6ykq Chain A Residue 1101 [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]
PDB6ykq Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		M40 F41 P42 Y43 H49 H52 N55 Y56 D80 G543 G544 E546 H547 H551 M582 V583 K634 M635
Binding residue
(residue number reindexed from 1)		M40 F41 P42 Y43 H49 H52 N55 Y56 D80 G543 G544 E546 H547 H551 M582 V583 K628 M629
Annotation score1
Binding affinityMOAD: Ki=52.36nM
Enzymatic activity
Catalytic site (original residue number in PDB) F41 D80 F507 H547 F557 K634 K637
Catalytic site (residue number reindexed from 1) F41 D80 F507 H547 F557 K628 K631
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004823 leucine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
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:6ykq, PDBe:6ykq, PDBj:6ykq
PDBsum6ykq
PubMed33248851
UniProtQ5FAJ3|SYL_NEIG1 Leucine--tRNA ligase (Gene Name=leuS)

[Back to BioLiP]