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BMRB: 15613

2K4L

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

Authors

Antonow, D., Barata, T., Jenkins, T.C., Parkinson, G.N., Howard, P.W., Thurston, D.E., Zloh, M.

Assembly

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'

Entity

1. DNA AATCTTTAAAGATT (polymer, Thiol state: not present), 14 monomers, 4340.799 × 2 Da Detail

AATCTTTAAA GATT

2. PZD (non-polymer), 386.443 × 2 Da

Total weight

9454.483 Da

Max. entity weight

4340.799 Da

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 79.9 %, Completeness (bb): 75.5 % Detail

Polymer type: polydeoxyribonucleotide

	Total	¹H
All	79.9 % (107 of 134)	79.9 % (107 of 134)
Suger, PO4	75.5 % (74 of 98)	75.5 % (74 of 98)
Nucleobase	91.7 % (33 of 36)	91.7 % (33 of 36)
Aromatic	92.9 % (26 of 28)	92.9 % (26 of 28)
Methyl	100.0 % (6 of 6)	100.0 % (6 of 6)

1. DNA AATCTTTAAAGATT

AATCTTTAAA GATT

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.85, Details The 0.68 mM DNA solution was incubated with PZD(7.5 mg as a slurry) at room temperature for 48 h under gentle shaking. The excess PZD was removed by filtration (Millipore 25 mm syringe filters, 0.45 m pore size) and the filtrated was collected in the NMR tube. This purification method was verified by repeating the procedure with PZD in D2O ,where filtrate showed no peaks even with higher number of scans (1048).

#	Name	Isotope labeling	Concentration
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')	natural abundance	0.68 mM
2	PZD_1		0.68 mM
3	sodium phosphate		10 mM
4	sodium chloride		100 mM
5	D2O	[U-100% 2H]	10 %
6	H2O		90 %

Release date

2008-06-25

Citation

Parallel synthesis of a novel C2-aryl pyrrolo[2,1-c][1,4]benzodiazepine (PBD) library
Antonow, D., Cooper, N., Howard, P.W., Thurston, D.E.
J. Comb. Chem. (2007), 9, 437-445, PubMed 17397227 , DOI 10.1021/cc0601332 , Abstract

Experiments performed 3 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.85, Details The 0.68 mM DNA solution was incubated with PZD(7.5 mg as a slurry) at room temperature for 48 h under gentle shaking. The excess PZD was removed by filtration (Millipore 25 mm syringe filters, 0.45 m pore size) and the filtrated was collected in the NMR tube. This purification method was verified by repeating the procedure with PZD in D2O ,where filtrate showed no peaks even with higher number of scans (1048).

#	Name	Isotope labeling	Concentration
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')	natural abundance	0.68 mM
2	PZD_1		0.68 mM
3	sodium phosphate		10 mM
4	sodium chloride		100 mM
5	D2O	[U-100% 2H]	10 %
6	H2O		90 %

2 2D 1H-1H COSY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
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')	natural abundance	0.68 mM
2	PZD_1		0.68 mM
3	sodium phosphate		10 mM
4	sodium chloride		100 mM
5	D2O	[U-100% 2H]	10 %
6	H2O		90 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
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')	natural abundance	0.68 mM
2	PZD_1		0.68 mM
3	sodium phosphate		10 mM
4	sodium chloride		100 mM
5	D2O	[U-100% 2H]	10 %
6	H2O		90 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15613_2k4l.nef
Input source #2: Coordindates	2k4l.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:11:DG:N2	3:1:PZD:C9A	unknown	unknown	n/a
2:11:DG:N2	3:2:PZD:C9A	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	PZD	(11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one	Assigned chemical shifts
C	2	PZD	(11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10----
AATCTTTAAAGATT
||||||||||||||
AATCTTTAAAGATT

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------30----
AATCTTTAAAGATT
||||||||||||||
AATCTTTAAAGATT
--------10----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	14	0	0	100.0
B	B	14	0	0	100.0

Content subtype: combined_15613_2k4l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	126		100.0 (chain: A, length: 14), 50.0 (chain: C, length: 2)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	296 (1)	noe	100.0 (chain: A, length: 14), 100.0 (chain: B, length: 14)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 14, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 2, Sequence coverage: 50.0%
- Total number of assignments
  - ¹H chemical shifts: 126
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: C
- Histogram of normalized assigned chemical shifts

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	DA	H61	6.01
11	DG	H21	8.32

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	134	107	79.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	74	75.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	33	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	6	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	13	13	100.0

Comp_index_ID	Comp_ID
1	PZD
2	PZD

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 14, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 14, Sequence coverage: 100.0%
- Total number of restraints: 296
- Weight of restraints: 1.0 (296)
- Potential type of restraints: square-well-parabolic (296)
- Range of distance target values: 2.35, 3.65 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
    None
- Distance restraints on contact map

Keywords anticancer, Pyrrolo[2, 1-c][1, 4]benzodiazepine

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Found 1 Document (0.489 seconds)

BMRB: 15613

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail