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- PDB-4b1f: Design of Inhibitors of Helicobacter pylori Glutamate Racemase as... -

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Basic information

Entry
Database: PDB / ID: 4b1f
TitleDesign of Inhibitors of Helicobacter pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / IMPROVED BIOAVAILABILITY
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / identical protein binding
Similarity search - Function
Glutamate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Glutamate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-GLUTAMIC ACID / Chem-KRH / Glutamate racemase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBasarab, G.S. / Hill, P. / Eyermann, C.J. / Gowravaram, M. / Kack, H. / Osimoni, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Design of Inhibitors of Helicobacter Pylori Glutamate Racemase as Selective Antibacterial Agents: Incorporation of Imidazoles Onto a Core Pyrazolopyrimidinedione Scaffold to Improve Bioavailabilty.
Authors: Basarab, G.S. / Hill, P. / Eyermann, C.J. / Gowravaram, M. / Kack, H. / Osimoni, E.
History
DepositionJul 10, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2May 2, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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

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Assembly

Deposited unit
A: GLUTAMATE RACEMASE
B: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2446
Polymers57,0642
Non-polymers1,1794
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-15.4 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.933, 75.974, 108.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAMATE RACEMASE


Mass: 28532.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ZLT0, glutamate racemase
#2: Chemical ChemComp-KRH / 5-methyl-3-(1-methyl-1H-imidazol-5-yl)-7-(2-methylpropyl)-2-(naphthalen-1-ylmethyl)-2H-pyrazolo[3,4-d]pyrimidine-4,6(5H,7H)-dione


Mass: 442.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H26N6O2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 1.064
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 2.05→6 Å / Num. obs: 29091 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→24.67 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.882 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23931 1574 5.1 %RANDOM
Rwork0.18517 ---
obs0.18796 29091 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.38 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 86 221 4331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194212
X-RAY DIFFRACTIONr_bond_other_d0.0010.024060
X-RAY DIFFRACTIONr_angle_refined_deg1.832.0075726
X-RAY DIFFRACTIONr_angle_other_deg0.85139386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.80225.06166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47115724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.107158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02878
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 94 -
Rwork0.279 1884 -
obs--84.28 %
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)
11.227-0.8214-0.0470.6284-0.2260.8503-0.16990.06340.06230.0823-0.0445-0.10480.0989-0.00080.21440.06330.0088-0.00630.0183-0.00340.0827.4-12.743-13.456
20.3311-0.16940.14350.38220.33171.28160.05340.0353-0.0090.02810.00840.0246-0.0441-0.0983-0.06180.05490.03110.01250.05590.02320.07453.6811.588-12.327
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2B1 - 255

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