Structure of PDB 6hb7 Chain B Binding Site BS01

Receptor Information
>6hb7 Chain B (length=413) Species: 469008 (Escherichia coli BL21(DE3)) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNLIKQLQERGLVAQVTDEEALAERLAQGPIALYCGFDPTADSLHLGHLV
PLLCLKRFQQAGHKPVALVGGATGLIGDPSFKAAERKLNTEETVQEWVDK
IRKQVAPFLDFDCGENSAIAANNYDWFGNMNVLTFLRDIGKHFSVNQMIN
KEAVKQRLNREDQGISFTEFSYNLLQGYDFACLNKQYGVVLQIGGSDQWG
NITSGIDLTRRLHQNQVFGLTVPLITKADGTAVWLDPKKTSPYKFYQFWI
NTADADVYRFLKFFTFMSIEEINALEEEDKNSGKAPRAQYVLAEQVTRLV
HGEEGLQAAKRITECLFSGSLSALSEADFEQLAQDGVPMVEMEKGADLMQ
ALVDSELQPSRGQARKTIASNAITINGEKQSDPEYFFKEEERLFGRFTLL
RRGKKNYCLICWK
Ligand information
Ligand IDY3U
InChIInChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1
InChIKeyJZICRHJSYJTEMP-IQNGCQKYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(Cc3ccc(cc3)O)N)O)O
OpenEye OEToolkits 2.0.6CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O
CACTVS 3.385CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)Cc3ccc(O)cc3)[C@@H](O)[C@H]2O)C1=O
CACTVS 3.385CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)Cc3ccc(O)cc3)[CH](O)[CH]2O)C1=O
FormulaC19 H24 N4 O10 S
Name[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate
ChEMBLCHEMBL4518549
DrugBank
ZINC
PDB chain6hb7 Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6hb7 Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y37 G39 D41 G50 H51 P54 L71 D81 Y175 Q179 D182 G197 G198 D200 Q201 L227
Binding residue
(residue number reindexed from 1)		Y34 G36 D38 G47 H48 P51 L68 D78 Y172 Q176 D179 G194 G195 D197 Q198 L224
Annotation score1
Binding affinityBindingDB: Ki=149nM
Enzymatic activity
Catalytic site (original residue number in PDB) T43 H48 H51 K85 R89 Q179 D200
Catalytic site (residue number reindexed from 1) T40 H45 H48 K82 R86 Q176 D197
Enzyme Commision number 6.1.1.1: tyrosine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004831 tyrosine-tRNA ligase activity
GO:0005524 ATP binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006437 tyrosyl-tRNA aminoacylation
GO:0043039 tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6hb7, PDBe:6hb7, PDBj:6hb7
PDBsum6hb7
PubMed30995568
UniProtP0AGJ9|SYY_ECOLI Tyrosine--tRNA ligase (Gene Name=tyrS)

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