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- PDB-2ky7: NMR Structural Studies on the Covalent DNA Binding of a Pyrrolobe... -

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Basic information

Entry
Database: PDB / ID: 2ky7
TitleNMR Structural Studies on the Covalent DNA Binding of a Pyrrolobenzodiazepine-Naphthalimide Conjugate
Components5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
KeywordsDNA / DNA duplex / Pyrrolobenzodiazepine / PBD-naphthalimide hybrid / DNA-drug complex
Function / homologyChem-HY2 / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average and energy minimized, model 1
AuthorsRettig, M. / Langel, W. / Kamal, A. / Weisz, K.
CitationJournal: Org.Biomol.Chem. / Year: 2010
Title: NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine-naphthalimide conjugate
Authors: Rettig, M. / Langel, W. / Kamal, A. / Weisz, K.
History
DepositionMay 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 2, 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)6,6843
Polymers6,0862
Non-polymers5981
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210.2 Å2
ΔGint-4.7 kcal/mol
Surface area3968.6 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 20000representative conformers of production runs
RepresentativeModel #1closest to the average and energy minimized

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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-HY2 / 2-{2-[4-(3-{[(11aS)-7-methoxy-5-oxo-2,3,5,10,11,11a-hexahydro-1H-pyrrolo[2,1-c][1,4]benzodiazepin-8-yl]oxy}propyl)piperazin-1-yl]ethyl}-1H-benzo[de]isoquinoline-1,3(2H)-dione


Mass: 597.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39N5O5
Nonpolymer detailsTHE LIGAND HY2 IS REFERRED AS PBD-NAPHTHALIMIDE HYBRID IN THE ARTICLE. THE HY2 IS NEUTRAL BUT ...THE LIGAND HY2 IS REFERRED AS PBD-NAPHTHALIMIDE HYBRID IN THE ARTICLE. THE HY2 IS NEUTRAL BUT BECAME PROTONATED WHEN BOUND TO DNA IN THE BUFFER USED. IN THIS ENTRY, EXTRA HYDROGEN HN16 IS INCLUDED TO THE COMPLEX COORDINATES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D DQF-COSY
2422D 1H-1H TOCSY
2522D-1H-1H ROESY
2622D 31P-1H HETCOR

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 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% D2O
21mM 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
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-11
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid-21
100 mMsodium chloride-31
20 mMsodium phosphate-41
1 mMDNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-52
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid-62
100 mMsodium chloride-72
20 mMsodium phosphate-82
Sample conditionsIonic strength: 0.28 / pH: 7 / Pressure: ambient / Temperature: 298 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 software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrestrained molecular dynamics
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average and energy minimized
NMR ensembleConformer selection criteria: representative conformers of production runs
Conformers calculated total number: 20000 / Conformers submitted total number: 5 / Representative conformer: 1

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