Structure of PDB 4k47 Chain A Binding Site BS01

Receptor Information
>4k47 Chain A (length=183) Species: 561276 (Streptococcus pneumoniae ATCC 700669) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGANVTFKVKGTDKEFTVFTTRPDTLFGATFTVLAPEHELVDAITSSEQA
EAVADYKHQASLKSDLVRTDLAKEKTGVWTGAYAINPVNGKEMPIWIADY
VLASYGTGAVMAVPAHDQRDWEFAKQFDLPIVEVLEGGNVEEAAYTEDGL
HVNSDFLDGLNKEDAIAKIVASLEEKGCGQEKV
Ligand information
Ligand IDWMP
InChIInChI=1S/C24H24BN5O9P/c26-22-18-23(28-11-27-22)30(12-29-18)24-21-20(17(37-24)10-36-40(32,33)34)38-25(39-21)16-8-14(6-7-15(16)9-35-25)19(31)13-4-2-1-3-5-13/h1-8,11-12,17,19-21,24,31H,9-10H2,(H2,26,27,28)(H2,32,33,34)/q-1/t17-,19+,20-,21+,24+,25-/m0/s1
InChIKeyXRLFSRQDERUGQF-ZZEVEECHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@@H](CO[P](O)(O)=O)[C@@H]4O[B-]5(OCc6ccc(cc56)[C@H](O)c7ccccc7)O[C@@H]34
OpenEye OEToolkits 1.7.6[B-]12(c3cc(ccc3CO1)C(c4ccccc4)O)OC5C(OC(C5O2)n6cnc7c6ncnc7N)COP(=O)(O)O
OpenEye OEToolkits 1.7.6[B-]12(c3cc(ccc3CO1)[C@@H](c4ccccc4)O)O[C@H]5[C@@H](O[C@H]([C@@H]5O2)n6cnc7c6ncnc7N)COP(=O)(O)O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH]4O[B-]5(OCc6ccc(cc56)[CH](O)c7ccccc7)O[CH]34
FormulaC24 H24 B N5 O9 P
Name[(1R,5R,6R,8S)-6-(6-aminopurin-9-yl)-3'-[(R)-oxidanyl(phenyl)methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1,3,5-triene]-8-yl]methyl dihydrogen phosphate
ChEMBL
DrugBank
ZINCZINC000263621231
PDB chain4k47 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4k47 Discovery of a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-tRNA synthetase
Resolution2.02 Å
Binding residue
(original residue number in PDB)
T247 T248 R249 V328 L329 Y332 V337 H343 D344 T373
Binding residue
(residue number reindexed from 1)
T20 T21 R22 V101 L102 Y105 V110 H116 D117 T146
Annotation score2
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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:4k47, PDBe:4k47, PDBj:4k47
PDBsum4k47
PubMed23959225
UniProtB8ZKS5|SYL_STRPJ Leucine--tRNA ligase (Gene Name=leuS)

[Back to BioLiP]