BMRB Entry 19592

Name: Molecular Binding of TFF1 Estrogen Response Element by a DNA Bis-intercalating Anticancer Drug XR5944
Published: 2014-04-11

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PDB ID: 2mg8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR19592
MolProbity Validation Chart

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

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Title:

Molecular Binding of TFF1 Estrogen Response Element by a DNA Bis-intercalating Anticancer Drug XR5944

Deposition date:

2013-10-30

Original release date:

2014-04-11

Authors:

Lin, Clement

Citation:

Citation: Lin, Clement; Mathad, Raveendra; Zhang, Zhenjiang; Sidell, Neil; Yang, Danzhou. "Solution structure of a 2:1 complex of anticancer drug XR5944 with TFF1 estrogen response element: insights into DNA recognition by a bis-intercalator." Nucleic Acids Res. 42, 6012-6024 (2014).
PubMed: 24711371

Assembly members:

Assembly members:
DNA_Strand_1, polymer, 15 residues, Formula weight is not available
DNA_Strand_2, polymer, 15 residues, Formula weight is not available
1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM, non-polymer, 590.718 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_Strand_1: AGGTCACGGTGGCCA
DNA_Strand_2: TGGCCACCGTGACCT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	287

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	5'-D(APGPGPTPCPAPCPGPGPTPGPGPCPCP*A)-3'	1
2	5'-D(TPGPGPCPCPAPCPCPGPTPGPAPCPCP*T)-3'	2
3	XR5944, 1	3
4	XR5944, 2	3

Entities:

Entity 1, 5'-D(*AP*GP*GP*TP*CP*AP*CP*GP*GP*TP*GP*GP*CP*CP*A)-3' 15 residues - Formula weight is not available

1

DA

DG

DT

DC

DA

DC

DG

DT

2

DG

DC

DA

Entity 2, 5'-D(*TP*GP*GP*CP*CP*AP*CP*CP*GP*TP*GP*AP*CP*CP*T)-3' 15 residues - Formula weight is not available

1

DT

DG

DC

DA

DC

DG

DT

2

DG

DA

DC

DT

Entity 3, XR5944, 1 - C34 H38 N8 O2 - 590.718 Da.

1

XR2

Samples:

sample_1: DNA (5'-D(*(X)*(X))-3')200 – 300 uM; sodium phosphate 50 mM; D2O 100%

sample_conditions_1: ionic strength: 50 mM; pH: 7; pressure: 1 atm; temperature: 273 K

Experiments:

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

Software:

XWINNMR, Bruker Biospin - collection

SPARKY, Goddard - chemical shift assignment

X-PLOR, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 600 MHz