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- PDB-7bzj: The Discovery of Benzhydrol-Oxaborole Hybrid Derivatives as Leucy... -

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Basic information

Entry
Database: PDB / ID: 7bzj
TitleThe Discovery of Benzhydrol-Oxaborole Hybrid Derivatives as Leucyl-tRNA Synthetase Inhibitors
ComponentsLeucine--tRNA ligase
KeywordsRNA BINDING PROTEIN/INHIBITOR / Leucyl-tRNA Synthetase / Pneumonia / RNA BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / Aminoacyl-tRNA synthetase, class Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-FGX / Leucine--tRNA ligase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiu, R.J. / Li, H. / Wang, E.D. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770842 China
National Natural Science Foundation of China (NSFC)31971230 China
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: Discovery of benzhydrol-oxaborole derivatives as Streptococcus pneumoniae leucyl-tRNA synthetase inhibitors.
Authors: Hao, G. / Li, H. / Yang, F. / Dong, D. / Li, Z. / Ding, Y. / Pan, W. / Wang, E. / Liu, R. / Zhou, H.
History
DepositionApr 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7472
Polymers21,0911
Non-polymers6551
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8900 Å2
Unit cell
Length a, b, c (Å)87.373, 87.373, 135.528
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-755-

HOH

21A-759-

HOH

31A-771-

HOH

41A-784-

HOH

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Components

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 21091.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC 700669 / Spain 23F-1) (bacteria)
Strain: ATCC 700669 / Spain 23F-1 / Gene: leuS, SPN23F02440 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZKS5, leucine-tRNA ligase
#2: Chemical ChemComp-FGX / [(1~{R},5~{R},6~{S},8~{R})-8-(6-aminopurin-9-yl)-4'-[(~{R})-oxidanyl-[4-(2-oxidanylidenepropylsulfanyl)phenyl]methyl]spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,7'-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-6-yl]methoxy-tris(oxidanyl)phosphanium


Mass: 655.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C28H31BN5O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris (pH5.5), 2.1M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21319 / % possible obs: 100 % / Redundancy: 34.2 % / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.033 / Rrim(I) all: 0.199 / Χ2: 0.978 / Net I/σ(I): 4.3 / Num. measured all: 728749
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0321.81.46210410.9170.3171.4970.92799.9
2.03-2.0724.11.32310460.9440.2721.3510.974100
2.07-2.1127.11.13910190.9640.2211.160.964100
2.11-2.1529.61.05310500.9610.1951.0710.96100
2.15-2.230.80.91510320.9710.1660.931.077100
2.2-2.2531.50.84510550.9750.1510.8590.936100
2.25-2.3131.70.7710450.9720.1370.7830.982100
2.31-2.3735.40.68910380.9850.1160.6991.072100
2.37-2.4437.40.61210460.9870.10.621.008100
2.44-2.5238.40.53610490.9960.0870.5430.973100
2.52-2.6138.50.45110480.9930.0730.4570.993100
2.61-2.7137.90.37910620.9930.0620.3841.048100
2.71-2.8436.10.30110520.9970.050.3051.014100
2.84-2.9939.30.23310700.9970.0370.2360.979100
2.99-3.1739.10.18510650.9980.030.1871.06100
3.17-3.4238.90.13210680.9980.0210.1331.024100
3.42-3.7636.10.10410890.9980.0170.1061.023100
3.76-4.3139.20.08710950.9990.0140.0880.969100
4.31-5.43360.07111250.9990.0120.0720.844100
5.43-5033.80.05912240.9990.010.060.73199.9

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Processing

Software
NameVersionClassification
PHENIXV1.18refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K48

4k48


Resolution: 2→31.4 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 1092 5.14 %
Rwork0.1879 20141 -
obs0.1893 21233 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.85 Å2 / Biso mean: 29.2203 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 2→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 76 190 1667
Biso mean--36.77 36.1 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.090.2751370.230124622599100
2.09-2.20.25781160.213724602576100
2.2-2.340.24191650.203624362601100
2.34-2.520.29561280.199624972625100
2.52-2.780.20671430.198824782621100
2.78-3.180.22541370.199225232660100
3.18-40.19591330.162825692702100
4-31.40.18171330.17682716284999

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