BMRB Entry 15613

Name: SOLUTION STRUCTURE OF THE BIS-C2-2-NAPHTHYLPYRROLO[2,1-c][1,4]BENZODIAZEPINE (DA046) DNA ADDUCT: THE MOLECULAR BASIS FOR DNA HELIX STABILIZATION.
Published: 2008-06-26

Click here to enlarge.

PDB ID: 2k4l
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR15613
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

SOLUTION STRUCTURE OF THE BIS-C2-2-NAPHTHYLPYRROLO[2,1-c][1,4]BENZODIAZEPINE (DA046) DNA ADDUCT: THE MOLECULAR BASIS FOR DNA HELIX STABILIZATION.

Deposition date:

2008-01-02

Original release date:

2008-06-26

Authors:

Antonow, Dyeison; Barata, Teresa; Jenkins, Terence; Parkinson, Gary; Howard, Philip; Thurston, David; Zloh, Mire

Citation:

Citation: Antonow, Dyeison; Cooper, Nectaroula; Howard, Philip; Thurston, David. "Parallel Synthesis of a Novel C2-Aryl Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) Library" J. Comb. Chem. 9, 437-445 (2007).
PubMed: 17397227

Assembly members:

Assembly members:
DNA_AATCTTTAAAGATT, polymer, 14 residues, 2338.598 Da.
PZD, non-polymer, 386.443 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA_AATCTTTAAAGATT: AATCTTTAAAGATT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	138

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DNA (5'-D((DA)P(DA)P(DT)P(DC)P(DT)P(DT)P(DT)P(DA)P(DA)P(DA)P(DG)P(DA)P(DT)P(DT))-3')_1	1
2	DNA (5'-D((DA)P(DA)P(DT)P(DC)P(DT)P(DT)P(DT)P(DA)P(DA)P(DA)P(DG)P(DA)P(DT)P(DT))-3')_2	1
3	PZD_1	2
4	PZD_2	2

Entities:

Entity 1, DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3')_1 14 residues - 2338.598 Da.

1

DA

DT

DC

DT

DA

2

DG

DA

DT

Entity 2, PZD_1 - C24 H22 N2 O3 - 386.443 Da.

1

PZD

Samples:

sample_1: DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3') 0.68 mM; PZD_1 0.68 mM; sodium phosphate 10 mM; sodium chloride 100 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_conditions_1: ionic strength: 130 mM; pH: 6.85; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH v2.16, Schwieters, Kuszewski, Tjandra and Clore - refinement

TOPSPIN v1.3, Bruker Biospin - collection, processing

AMIX v3.5.5, Bruker Biospin - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 500 MHz