3GHC

Design, Synthesis, and X-ray Crystal Structure of Classical and Nonclassical 2-amino-4-oxo-5-substituted-6-thieno[2,3-d]pyrimidines as dual thymidylate synthase and dihydrofolate reductase inhibitors and as potential antitumor agenst


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72PDB entry 1u72

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.9298100 mN KPO4, pH 6.9, 30% sat. AmSO4, 3% v/v ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.550.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.356α = 90
b = 84.356β = 90
c = 77.767γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDMARMOSAIC 325 mm CCDmirrors2008-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9422SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.353.2299.80.0450.0225.350745481642214.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3799.30.1430.07510.34.37389

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1u721.322.51215074548155257799.840.171430.170030.1985RANDOM14.473
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.77
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg13.483
r_dihedral_angle_1_deg6.372
r_scangle_it5.253
r_scbond_it3.432
r_angle_refined_deg2.58
r_mcangle_it2.291
r_mcbond_it1.346
r_chiral_restr0.551
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.77
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg13.483
r_dihedral_angle_1_deg6.372
r_scangle_it5.253
r_scbond_it3.432
r_angle_refined_deg2.58
r_mcangle_it2.291
r_mcbond_it1.346
r_chiral_restr0.551
r_bond_refined_d0.032
r_gen_planes_refined0.018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1517
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms95

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling