Structure of PDB 5agr Chain A Binding Site BS01

Receptor Information
>5agr Chain A (length=190) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAVALFSARAVDIEVFTTRPDTLFGATYLVLAPEHDLVDELVAASWPAGV
NPLWTYGGGTPGEAIAAYRRAIAAKSDLERQKTGVFLGSYAINPANGEPV
PIFIADYVLAGYGTGAIMAVPGHDQRDWDFARAFGLPIVEVIAGGNISES
AYTGDGILVNSDYLNGMSVPAAKRAIVDRLESAGRGRARI
Ligand information
Ligand IDA52
InChIInChI=1S/C20H25BN6O9P/c1-2-31-11-5-3-4-10-12(6-22)34-21(14(10)11)35-16-13(7-32-37(28,29)30)33-20(17(16)36-21)27-9-26-15-18(23)24-8-25-19(15)27/h3-5,8-9,12-13,16-17,20H,2,6-7,22H2,1H3,(H2,23,24,25)(H2,28,29,30)/q-1/p-2/t12-,13-,16-,17-,20-,21+/m1/s1
InChIKeyWLOBNXOMDQETEC-IMBSHPNCSA-L
SMILES
SoftwareSMILES
CACTVS 3.385CCOc1cccc2[C@@H](CN)O[B-]3(O[C@@H]4[C@@H](CO[P]([O-])([O-])=O)O[C@H]([C@@H]4O3)n5cnc6c(N)ncnc56)c12
OpenEye OEToolkits 1.7.6[B-]12(c3c(cccc3OCC)[C@H](O1)CN)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)([O-])[O-]
CACTVS 3.385CCOc1cccc2[CH](CN)O[B-]3(O[CH]4[CH](CO[P]([O-])([O-])=O)O[CH]([CH]4O3)n5cnc6c(N)ncnc56)c12
OpenEye OEToolkits 1.7.6[B-]12(c3c(cccc3OCC)C(O1)CN)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)([O-])[O-]
FormulaC20 H23 B N6 O9 P
Name3-AMINOMETHYL-7-(ETHOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine
ChEMBL
DrugBank
ZINC
PDB chain5agr Chain A Residue 1514 [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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PDB5agr Discovery of Novel Oral Protein Synthesis Inhibitors of Mycobacterium Tuberculosis that Target Leucyl-tRNA Synthetase.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		F335 T336 T337 R338 V431 L432 Y435 I440 M441 D447 R449 D450
Binding residue
(residue number reindexed from 1)		F16 T17 T18 R19 V108 L109 Y112 I117 M118 D124 R126 D127
Annotation score2
Binding affinityPDBbind-CN: -logKd/Ki=5.43,Kd=3.7uM
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:0004823 leucine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation

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Molecular Function
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Biological Process
External links
PDB RCSB:5agr, PDBe:5agr, PDBj:5agr
PDBsum5agr
PubMed27503647
UniProtP9WFV1|SYL_MYCTU Leucine--tRNA ligase (Gene Name=leuS)

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