6BRF

Tubulin-RB3_SLD-TTL in complex with heterocyclic pyrimidine compound 4b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Heterocyclic-Fused Pyrimidines as Novel Tubulin Polymerization Inhibitors Targeting the Colchicine Binding Site: Structural Basis and Antitumor Efficacy.

Banerjee, S.Arnst, K.E.Wang, Y.Kumar, G.Deng, S.Yang, L.Li, G.B.Yang, J.White, S.W.Li, W.Miller, D.D.

(2018) J. Med. Chem. 61: 1704-1718

  • DOI: 10.1021/acs.jmedchem.7b01858
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the design, synthesis, and biological evaluation of heterocyclic-fused pyrimidines as tubulin polymerization inhibitors targeting the colchicine binding site with significantly improved therapeutic index. Additionally, for the first time, w ...

    We report the design, synthesis, and biological evaluation of heterocyclic-fused pyrimidines as tubulin polymerization inhibitors targeting the colchicine binding site with significantly improved therapeutic index. Additionally, for the first time, we report high-resolution X-ray crystal structures for the best compounds in this scaffold, 4a, 4b, 6a, and 8b. These structures not only confirm their direct binding to the colchicine site in tubulin and reveal their detailed molecular interactions but also contrast the previously published proposed binding mode. Compounds 4a and 6a significantly inhibited tumor growth in an A375 melanoma xenograft model and were accompanied by elevated levels of apoptosis and disruption of tumor vasculature. Finally, we demonstrated that compound 4a significantly overcame clinically relevant multidrug resistance in a paclitaxel resistant PC-3/TxR prostate cancer xenograft model. Collectively, these studies provide preclinical and structural proof of concept to support the continued development of this scaffold as a new generation of tubulin inhibitors.


    Organizational Affiliation

    Structural Biology Department, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital , Memphis, Tennessee 38105, United States.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center , Memphis, Tennessee 38163, United States.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy , Chengdu 610041, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C
450Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Go to Gene View: TUBA1B
Go to UniProtKB:  Q2XVP4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B, D
445Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
143Homo sapiensMutation(s): 0 
Gene Names: STMN4
Find proteins for Q9H169 (Homo sapiens)
Go to Gene View: STMN4
Go to UniProtKB:  Q9H169
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tubulin tyrosine ligase
F
384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Go to Gene View: TTL
Go to UniProtKB:  E1BQ43
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E44
Query on E44

Download SDF File 
Download CCD File 
B, D
2-chloro-4-(6-methoxy-3,4-dihydroquinolin-1(2H)-yl)pyrido[3,2-d]pyrimidine
C17 H15 Cl N4 O
QDLGKFNCVHBEOQ-UHFFFAOYSA-N
 Ligand Interaction
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, C
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

Download SDF File 
Download CCD File 
F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.129α = 90.00
b = 157.747β = 90.00
c = 181.596γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA148706

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection