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PDB ID: 9vzw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36774
MolProbity Validation Chart

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NMR-STAR v3 text 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

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Name: A solution NMR model of Z-form DNA binding with ligand CBL0137
Published: 2026-03-31

Title:

A solution NMR model of Z-form DNA binding with ligand CBL0137

Deposition date:

2025-07-23

Original release date:

2026-03-31

Authors:

Wang, S.; Liu, F.; Xu, Y.

Citation:

Citation: Liu, Feifan; Wang, Shiyu; Xu, Yan. "Solution structure of Z-form DNA bound to a curaxin ligand CBL0137." Nucleic Acids Res. 54, gkag104-gkag104 (2026).
PubMed: 41665010

Assembly members:

Assembly members:
DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3'), polymer, 12 residues, 1896.194 Da.
CBL0137, non-polymer, 336.427 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis Host organism: unidentified

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3'): CGCXCG

Data sets:

assigned_chemical_shifts
- D_1300061867_cs_P1.str.V1

Data type	Count
1H chemical shifts	50

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1_1	1
2	entity_1_2	1
3	entity_A1MA8	2

Entities:

Entity 1, entity_1_1 12 residues - 1896.194 Da.

1

DC

DG

DC

A1MA9

DC

DG

Entity 2, entity_A1MA8 - C21 H24 N2 O2 - 336.427 Da.

1

A1MA8

Samples:

sample_1: DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3') 6.0 mM; NaCl 2000 mM; Na-PO4 1 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3') 6.0 mM; NaCl 2000 mM; Na-PO4 1 mM; D2O, [U-2H], 100%

sample_3: DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3') 6.0 mM; NaCl 2000 mM; Na-PO4 1 mM; H2O 90%; D2O, [U-2H], 10%

sample_4: DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3') 6.0 mM; NaCl 2000 mM; Na-PO4 1 mM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 2.0 M; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
1D	sample_3	isotropic	sample_conditions_1
1D	sample_4	isotropic	sample_conditions_1
1D	sample_2	isotropic	sample_conditions_1

Software:

MestreLab (Mnova / MestReNova / MestReC), Carballas - chemical shift assignment

MestreLab (Mnova / MestReNova / MestReC), Carballas - chemical shift calculation

Discovery Studio, Martinez - structure calculation

TopSpin, Bruker Biospin - collection

Discovery Studio, Martinez - refinement

NMR spectrometers:

Bruker AVANCE III 500 MHz

BMRB Entry 36774