9VZW | pdb_00009vzw

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

• PDB DOI: https://doi.org/10.2210/pdb9VZW/pdb
• NAKB: 9VZW

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-23 Released: 2025-08-06 
• Deposition Author(s): Wang, S.Y., Liu, F.F., Xu, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Uncovering the structure of Z-form DNA-CBL0137 complex in vitro and in cells

Liu, F.F., Wang, S.Y., Xu, Y.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 4.47 kDa 
• Atom Count: 300 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*(FG)P*CP*G)-3')	A, B	6	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1MA8 (Subject of Investigation/LOI)	C [auth A], D [auth B]	CBL0137 C21 H24 N2 O2 JKCSODVERGVDLT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Currently 9VZW does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Wang, S.Y., Liu, F.F., Xu, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release