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- PDB-2y67: New 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD ... -

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Basic information

Entry
Database: PDB / ID: 2y67
TitleNew 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / CELL SHAPE / CELL WALL / CELL WALL BIOGENESIS/DEGRADATION / NUCLEOTIDE-BINDING / PEPTIDOGLYCAN SYNTHESIS / UMA
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase MurD-like, N-terminal domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N21 / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZidar, N. / Tomasic, T. / Sink, R. / Kovac, A. / Patin, D. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Muller-Premru, M. / Zega, A. ...Zidar, N. / Tomasic, T. / Sink, R. / Kovac, A. / Patin, D. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Muller-Premru, M. / Zega, A. / Gobec, S. / Peterlin-Masic, L. / Kikelj, D.
CitationJournal: Eur.J.Med.Chem / Year: 2011
Title: New 5-Benzylidenethiazolidin-4-One Inhibitors of Bacterial Murd Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation.
Authors: Zidar, N. / Tomasic, T. / Sink, R. / Kovac, A. / Patin, D. / Blanot, D. / Contreras-Martel, C. / Dessen, A. / Premru, M.M. / Zega, A. / Gobec, S. / Masic, L.P. / Kikelj, D.
History
DepositionJan 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5963
Polymers47,9791
Non-polymers6172
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.326, 65.326, 134.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / MURD LIGASE / D-GLUTAMIC ACID-ADDING ENZYME / UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE


Mass: 47979.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PABD16/MURD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA]
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-N21 / (2R)-2-[[4-[[4-[(Z)-(2,4-dioxo-1,3-thiazolidin-5-ylidene)methyl]phenoxy]methyl]phenyl]sulfonylamino]pentanedioic acid


Mass: 520.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N2O9S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.92 % / Description: NONE
Crystal growpH: 7.4
Details: 6.0 MG/ML MURD, 20 MM HEPES PH 7.4, 200MM NACL, 5MM DITHIOTHREITOL, 0.05% (W/V) NAN3, 0.1M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97238
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97238 Å / Relative weight: 1
ReflectionResolution: 1.85→46.89 Å / Num. obs: 45564 / % possible obs: 84.3 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Biso Wilson estimate: 40.14 Å2 / Rsym value: 0.04 / Net I/σ(I): 33.79
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.06 / Rsym value: 0.45 / % possible all: 55.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAG

1uag


Resolution: 1.85→46.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.744 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24852 4601 10.1 %RANDOM
Rwork0.208 ---
obs0.21211 40963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.663 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 40 221 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223411
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9834641
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56824.558147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27815563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8311522
X-RAY DIFFRACTIONr_chiral_restr0.1090.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6471.52178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.50823483
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.15631233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.0984.51151
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.484 259 -
Rwork0.48 2235 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5739-0.96941.70262.1574-0.02234.18410.2041-0.0675-0.1547-0.0993-0.00620.13170.4977-0.0131-0.19780.06870.0109-0.02310.04490.03580.052259.3872-3.099514.6877
21.0618-0.11890.72560.1996-0.26951.0104-0.064-0.05040.1757-0.05380.00640.0139-0.0741-0.06850.05760.0694-0.002-0.04210.04630.0010.086237.352913.43814.0095
33.10760.15890.03641.26460.16891.4215-0.017-0.2828-0.0311-0.0078-0.03460.02940.0758-0.11660.05160.01870.0076-0.01680.0968-0.01040.0324.12843.284526.2307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2A94 - 295
3X-RAY DIFFRACTION3A304 - 439

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