Structure of PDB 5usf Chain A Binding Site BS01

Receptor Information
>5usf Chain A (length=682) Species: 981087 (Leishmania donovani BPK282A1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMNTDERYKLLRSVGEECIQESELRNLIEKKPLIRCYDGFEPSGRMHIA
QGIFKAVNVNKCTAAGCEFVFWVADWFALMNDKVGGELEKIRIVGRYLIE
VWKAAGMDTDKVLFLWSSEEITSHADTYWRMVLDIGRQNTIARIKKCCTI
MGKTEGTLTAAQVLYPLMQCCDIFFLKADICQLGLDQRKVNMLAREYCDL
IGRKLKPVILSHHMLAGLRRGQAKMSKSDPDSAIFMEDTEEDVARKIRQA
YCPRVKQSASAITDDGAPVATDDRNPVLDYFQCVVYARPGAVAAIDGTTY
ATYEDLEQAFVSDEVSEDALKSCLIDEVNALLAPVRQHFASNEEAHELLE
AVKSYRKGGATLPLAETALPAAPEKPHACMWMPALLKVPLDVAEGMIKAT
EDFIAAHPGGTVTVVLPDWSAVASDEITGVEKDISAALQVNCALLKAYGL
PNSVKIVTENEVILGNRNDFWVSVIGIARKNLLSHIEELYGGELRNAGQV
IAALMRVATALMLSVSHVISTSLDGHINAFAREYTKERIECVQTLEGRIP
ALHRPGAAPAVLGADDVLYLDDNDMDIRRKIKKAYSAPNEEANPVISVAQ
HLLAQHGALNIERGEANGGNVSYNTPEALVADCGSGALHPADLKAAVLQL
LLDRSAQARALLNGELKKNMTALRNAEKKMAK
Ligand information
Ligand IDYSA
InChIInChI=1S/C19H23N7O8S/c20-11(5-9-1-3-10(27)4-2-9)18(30)25-35(31,32)33-6-12-14(28)15(29)19(34-12)26-8-24-13-16(21)22-7-23-17(13)26/h1-4,7-8,11-12,14-15,19,27-29H,5-6,20H2,(H,25,30)(H2,21,22,23)/t11-,12+,14+,15+,19+/m0/s1
InChIKeyMJZAZMKENKZBAJ-QTOWJTHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N)O
CACTVS 3.341N[CH](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34
CACTVS 3.341N[C@@H](Cc1ccc(O)cc1)C(=O)N[S](=O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34
OpenEye OEToolkits 1.5.0c1cc(ccc1CC(C(=O)NS(=O)(=O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N)O
ACDLabs 10.04O=C(NS(=O)(=O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)C(N)Cc4ccc(O)cc4
FormulaC19 H23 N7 O8 S
Name5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE;
TYROSYLADENYLATE
ChEMBLCHEMBL1163085
DrugBankDB03325
ZINCZINC000016052371
PDB chain5usf Chain A Residue 701 [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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PDB5usf Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		Y36 D37 G38 E40 A48 Q49 W70 F75 Y163 Q167 D170 L181 G182 Q185 H210 M212 L213
Binding residue
(residue number reindexed from 1)		Y38 D39 G40 E42 A50 Q51 W72 F77 Y165 Q169 D172 L183 G184 Q187 H212 M214 L215
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=9.16,IC50=0.69nM
Enzymatic activity
Enzyme Commision number 6.1.1.1: tyrosine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004831 tyrosine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006437 tyrosyl-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:5usf, PDBe:5usf, PDBj:5usf
PDBsum5usf
PubMed28427904
UniProtA0A3Q8ID88

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