2KY7

NMR Structural Studies on the Covalent DNA Binding of a Pyrrolobenzodiazepine-Naphthalimide Conjugate


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 90% H2O/10% D2O90% H2O/10% D2O0.287ambient298
22D 1H-1H NOESY1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
32D DQF-COSY1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
42D 1H-1H TOCSY1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
52D-1H-1H ROESY1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
62D 31P-1H HETCOR1mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriarepresentative conformers of production runs
Conformers Calculated Total Number20000
Conformers Submitted Total Number5
Representative Model1 (closest to the average and energy minimized)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1restrained molecular dynamicsAmber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
2refinementAmber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm