9U6A | pdb_00009u6a

Tubulin-DARPin D1 in complex with a flavone

• PDB DOI: https://doi.org/10.2210/pdb9U6A/pdb

• Classification: CELL CYCLE
• Organism(s): Sus scrofa, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-22 Released: 2025-04-16 
• Deposition Author(s): Yan, W., Yang, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure of quercetin 3,4'-dimethyl ether in complex with tubulin provides a rationale for drug design.

Su, Y., Yan, W., Yang, J., Yang, F.

(2025) Biochem Biophys Res Commun 777: 152245-152245

• PubMed: 40578283 
• DOI: https://doi.org/10.1016/j.bbrc.2025.152245
• Primary Citation Related Structures: 
  9U6A


• PubMed Abstract: 
  

  Microtubules, composed of αβ-tubulin heterodimers, serve as key targets for anticancer therapeutics due to their critical role in cell division. Numerous compounds have been discovered to interact with tubulin and disrupt microtubule dynamics, particularly those targeting the colchicine-binding domain. Certain flavones, for instance, have demonstrated the ability to bind to this site and suppress microtubule polymerization. Despite their potential, progress in developing flavone-based drugs has been limited by insufficient structural data on tubulin-ligand complexes. Here, we present the high-resolution (1.92 Å) crystal structure of tubulin in complex with a flavone derivative, quercetin 3,4'-dimethyl ether (QU34), elucidating the specific molecular interactions at atomic detail. By analyzing this structure alongside other colchicine-site inhibitors, we clarify prior structure-activity relationship (SAR) findings and offer a framework for designing optimized flavone analogs targeting this site.

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Organizational Affiliation: 
• College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China. Electronic address: [e-mail].
College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, 610041, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 118 kDa 
• Atom Count: 8,438 
• Modeled Residue Count: 1,015 
• Deposited Residue Count: 1,051 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A	451	Sus scrofa	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B	431	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed Ankyrin Repeat Protein (DARPIN) D1	C [auth F]	169	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	D [auth A], F [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
A1L8X (Subject of Investigation/LOI)	G [auth B]	3-methoxy-2-(4-methoxy-3-oxidanyl-phenyl)-5,7-bis(oxidanyl)chromen-4-one C17 H14 O7 ZSPZNFOLWQEVQJ-UHFFFAOYSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.6	α = 90
b = 91.08	β = 97.28
c = 83.17	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-16 
Deposition Author(s): Yan, W., Yang, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-04-16
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references