9MLF | pdb_00009mlf

TUBULIN-RB3_SLD IN COMPLEX WITH COMPOUND QW-4-183-llb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Design and synthesis of novel 4-aryl-2-benzoyl-imidazoles as colchicine binding site inhibitors.

Albadari, N.Xie, Y.Wang, Q.Miller, D.J.Gruntz, J.Q.Oldham, M.L.Chen, H.Ma, D.Wu, Z.Miller, D.D.Li, W.

(2025) Eur J Med Chem 298: 118021-118021

  • DOI: https://doi.org/10.1016/j.ejmech.2025.118021
  • Primary Citation of Related Structures:  
    9MLF

  • PubMed Abstract: 

    Highly potent tubulin inhibitors serve as critical payloads in several FDA-approved antibody-drug conjugates (ADCs). However, all these compounds are natural products with complex structures, which limit the ability to adjust their physicochemical properties for the optimal balance between payload release and ADC stability during systemic circulation, as well as efficient tumor penetration. Although taxanes are widely used in cancer therapy, they are unsuitable for ADCs due to insufficient potency and a high tendency to develop acquired drug resistance. Colchicine binding site inhibitors (CBSIs) are attractive alternatives, offering tunable properties and the potential to overcome multidrug resistance associated with the use of many existing tubulin inhibitors. However, most CBSIs lack sufficient potency for viable ADC applications. In our pursuit of a highly potent CBSI suitable for ADC use, we identified a novel series of sabizabulin derivatives. These compounds were evaluated in vitro across four cancer cell lines, including one with high resistance to taxanes. Among them, compound 11b emerged as the most promising one with IC 50 values ranging from 0.6 nM to 1.3 nM in cancer cells, entering the potency range as a potential ADC payload. Importantly, 11b also effectively overcame taxane-associated drug resistance. Mechanistic studies confirmed that 11b directly binds to the colchicine site on tubulin, as demonstrated by its high-resolution crystal structure in a complex with tubulin protein. In vivo efficacy studies using a taxane-resistant prostate cancer xenograft model (PC-3/TxR) revealed that 11b significantly suppressed tumor growth, disrupted angiogenesis, and induced apoptosis. Together, these findings highlight 11b as a highly potent CBSI with the capability of overcoming acquired drug resistance to taxanes, suggesting its strong potential as a next-generation ADC payload.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38163, United States; Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, 55473, Saudi Arabia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
438Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
433Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A287AGU7 (Sus scrofa)
Explore A0A287AGU7 
Go to UniProtKB:  A0A287AGU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287AGU7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63043
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A],
J [auth C]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
G [auth B],
M [auth D]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
A1BMG (Subject of Investigation/LOI)
Query on A1BMG

Download Ideal Coordinates CCD File 
H [auth B],
L [auth D]
[(4M)-4-(1H-indol-4-yl)-1H-imidazol-2-yl](3,4,5-trimethoxyphenyl)methanone
C21 H19 N3 O4
UBTWEWDUQYSFCL-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.482α = 90
b = 126.974β = 90
c = 252.074γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2025-11-12 
  • Deposition Author(s): Miller, D.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release