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- PDB-2ktt: Solution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzo... -

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Entry
Database: PDB / ID: 2ktt
TitleSolution Structure of a Covalently Bound Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid to a 10mer DNA Duplex
Components5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
KeywordsDNA / DNA duplex / Pyrrolobenzodiazepine / PBD-benzimidazole hybrid / DNA-drug complex
Function / homologyChem-PBH / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsRettig, M. / Weingarth, M. / Langel, W. / Kamal, A. / Kumar, P.P. / Weisz, K.
CitationJournal: Biochemistry / Year: 2009
Title: Solution structure of a covalently bound pyrrolo[2,1-c][1,4]benzodiazepine-benzimidazole hybrid to a 10mer DNA duplex.
Authors: Rettig, M. / Weingarth, M. / Langel, W. / Kamal, A. / Kumar, P.P. / Weisz, K.
History
DepositionFeb 8, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
B: 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6833
Polymers6,0862
Non-polymers5971
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 15000representative conformers of clusters
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'


Mass: 3043.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-PBH / (11aS)-7-methoxy-8-(3-{4-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]phenoxy}propoxy)-1,2,3,10,11,11a-hexahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one


Mass: 596.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H40N6O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D DQF-COSY
1312D 1H-1H TOCSY
2422D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-1, 1 mM Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid-2, 100 mM NaCl-3, 20 mM PO4-4, 100% D2O100% D2O
21 mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-5, 1 mM Pyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid-6, 100 mM NaCl-7, 20 mM PO4-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA1
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid-21
100 mMNaCl-31
20 mMPO4-41
1 mMDNA2
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Benzimidazole Hybrid-62
100 mMNaCl-72
20 mMPO4-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.287ambient 295 K
20.287ambient 283 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: Amber / Version: 9
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollm
Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: representative conformers of clusters
Conformers calculated total number: 15000 / Conformers submitted total number: 4 / Representative conformer: 1

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