7TTF | pdb_00007ttf

Tubulin-RB3_SLD in complex with compound 12k


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7TTF

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design, Synthesis, and Biological Evaluation of Pyrimidine Dihydroquinoxalinone Derivatives as Tubulin Colchicine Site-Binding Agents That Displayed Potent Anticancer Activity Both In Vitro and In Vivo.

Pochampally, S.Hartman, K.L.Wang, R.Wang, J.Yun, M.K.Parmar, K.Park, H.Meibohm, B.White, S.W.Li, W.Miller, D.D.

(2023) Acs Pharmacol Transl Sci 6: 526-545

  • DOI: https://doi.org/10.1021/acsptsci.2c00108
  • Primary Citation Related Structures: 
    7TTD, 7TTE, 7TTF

  • PubMed Abstract: 

    Polymerization of tubulin dimers to form microtubules is one of the key events in cell proliferation. The inhibition of this event has long been recognized as a potential treatment option for various types of cancer. Compound 1e was previously developed by our team as a potent inhibitor of tubulin polymerization that binds to the colchicine site. To further improve the potency and therapeutic properties of compound 1e , we hypothesized based on the X-ray crystal structure that modification of the pyrimidine dihydroquinoxalinone scaffold with additional hetero-atom (N, O, and S) substituents could allow the resulting new compounds to bind more tightly to the colchicine site and display greater efficacy in cancer therapy. We therefore synthesized a series of new pyrimidine dihydroquinoxalinone derivatives, compounds 10 , 12b-c , 12e , 12h , and 12j-l , and evaluated their cytotoxicity and relative ability to inhibit proliferation, resulting in the discovery of new tubulin-polymerization inhibitors. Among these, the most potent new inhibitor was compound 12k , which exhibited high cytotoxic activity in vitro, a longer half-life than the parental compound in liver microsomes (IC 50 = 0.2 nM, t 1/2 = >300 min), and significant potency against a wide range of cancer cell lines including those from melanoma and breast, pancreatic, and prostate cancers. High-resolution X-ray crystal structures of the best compounds in this scaffold series, 12e , 12j , and 12k , confirmed their direct binding to the colchicine site of tubulin and revealed their detailed molecular interactions. Further evaluation of 12k in vivo using a highly taxane-resistant prostate cancer xenograft model, PC-3/TxR, demonstrated the strong tumor growth inhibition at the low dose of 2.5 mg/kg (i.v., twice per week). Collectively, these results strongly support further preclinical evaluations of 12k as a potential candidate for development.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States.

Macromolecule Content 

  • Total Structure Weight: 215.16 kDa 
  • Atom Count: 14,849 
  • Modeled Residue Count: 1,829 
  • Deposited Residue Count: 1,885 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
433Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Stathmin-4143Rattus norvegicusMutation(s): 2 
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
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
F [auth A],
O [auth C],
Q [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
I [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
JV9
(Subject of Investigation/LOI)

Query on JV9



Download:Ideal Coordinates CCD File
J [auth B],
R [auth D]
7-methoxy-4-[2-(methylamino)-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-yl]-3,4-dihydroquinoxalin-2(1H)-one
C17 H19 N5 O2
BRTSQLXTBUCXNF-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
K [auth B]
L [auth B]
M [auth B]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
P [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.695α = 90
b = 126.407β = 90
c = 250.065γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA148706

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description