Structure of PDB 7yp8 Chain A Binding Site BS01

Receptor Information
>7yp8 Chain A (length=866) Species: 521006 (Neisseria gonorrhoeae NCCP11945) [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
NPADVELSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADTARL
FMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFAGNQ
DGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDKTDT
GSEQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPTVDE
AALVKSEIEVMVQVNGKLRGKITVAADASKADLEAAALANEGAVKFMEGK
PAKKIIVVPGRLVNIV
Ligand information
Ligand IDJIE
InChIInChI=1S/C17H26N6O7S/c1-8(2)5-9(18)16(26)22-31(27,28)29-6-11-13(24)14(25)17(30-11)23-7-21-12-10(23)3-4-20-15(12)19/h3-4,7-9,11,13-14,17,24-25H,5-6,18H2,1-2H3,(H2,19,20)(H,22,26)/t9-,11+,13+,14+,17+/m0/s1
InChIKeySLTGASQMUPNMPQ-JHTGIODLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)nccc23
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ccnc3N)O)O)N
CACTVS 3.385CC(C)C[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)nccc23
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2ccnc3N)O)O)N
FormulaC17 H26 N6 O7 S
Name[(2R,3S,4R,5R)-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl N-[(2S)-2-azanyl-4-methyl-pentanoyl]sulfamate
ChEMBL
DrugBank
ZINC
PDB chain7yp8 Chain A Residue 1002 [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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PDB7yp8 The essential role of a structured water in base recognition of Class II aminoacyl-tRNA synthetases
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F41 P42 Y43 G51 H52 N55 D80 S510 G543 G544 E546 H547 H551 Q580 M582 V583
Binding residue
(residue number reindexed from 1)		F41 P42 Y43 G51 H52 N55 D80 S510 G543 G544 E546 H547 H551 Q580 M582 V583
Annotation score1
Enzymatic activity
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7yp8, PDBe:7yp8, PDBj:7yp8
PDBsum7yp8
PubMed
UniProtB4RNT1|SYL_NEIG2 Leucine--tRNA ligase (Gene Name=leuS)

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