Structure of PDB 6ykx Chain A Binding Site BS01

Receptor Information
>6ykx Chain A (length=842) 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
NPADVELTSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADTAR
LFMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFAGN
QDGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDKTD
TGSEQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPTVD
EAALVKSEIEVMVQVNGKLADLEAAALANIIVVPGRLVNIVV
Ligand information
Ligand IDOW2
InChIInChI=1S/C26H41N7O8S/c1-17(2)11-21(27)25(36)31-42(38,39)41-16-22-24(35)23(34)19(15-40-22)9-6-10-33-14-20(30-32-33)13-29-26(37)28-12-18-7-4-3-5-8-18/h3-5,7-8,14,17,19,21-24,34-35H,6,9-13,15-16,27H2,1-2H3,(H,31,36)(H2,28,29,37)/t19-,21+,22-,23+,24-/m1/s1
InChIKeyBUJGEMBLEXNUBK-MENZVKOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NS(=O)(=O)OCC1C(C(C(CO1)CCCn2cc(nn2)CNC(=O)NCc3ccccc3)O)O)N
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](CO1)CCCn2cc(nn2)CNC(=O)NCc3ccccc3)O)O)N
CACTVS 3.385CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1OC[C@@H](CCCn2cc(CNC(=O)NCc3ccccc3)nn2)[C@H](O)[C@@H]1O
CACTVS 3.385CC(C)C[CH](N)C(=O)N[S](=O)(=O)OC[CH]1OC[CH](CCCn2cc(CNC(=O)NCc3ccccc3)nn2)[CH](O)[CH]1O
FormulaC26 H41 N7 O8 S
Name[(2~{R},3~{S},4~{S},5~{R})-3,4-bis(oxidanyl)-5-[3-[4-[[(phenylmethyl)carbamoylamino]methyl]-1,2,3-triazol-1-yl]propyl]oxan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate
ChEMBLCHEMBL4864835
DrugBank
ZINC
PDB chain6ykx 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

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PDB6ykx Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		M40 F41 P42 Y43 H49 H52 Y56 D80 S510 G543 G544 E546 H547 H551 M582 V583 M635 S636 K637
Binding residue
(residue number reindexed from 1)		M40 F41 P42 Y43 H49 H52 Y56 D80 S510 G543 G544 E546 H547 H551 M582 V583 M627 S628 K629
Annotation score1
Binding affinityMOAD: Ki=182.35nM
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 K626 K629
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ykx, PDBe:6ykx, PDBj:6ykx
PDBsum6ykx
PubMed33248851
UniProtQ5FAJ3|SYL_NEIG1 Leucine--tRNA ligase (Gene Name=leuS)

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