Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A4B1C1 

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

Macromolecule Content

• Total Structure Weight: 265.19 kDa 
• Atom Count: 18092 
• Residue Count: 2171 
• Unique protein chains: 4

5M7E

Tubulin-BKM120 complex

• DOI: 10.2210/pdb5M7E/pdb

• Classification: CELL CYCLE
• Organism(s): Bos taurus, Rattus norvegicus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-27 Released: 2017-02-22 
• Deposition Author(s): Bohnacker, T., Prota, A.E., Steinmetz, M.O., Wymann, M.P.
• Funding Organization(s): Swiss Commission for Technology and Innovation (CTI), Stiftung fuer Krebsbekaempfung, Swiss National Science Foundation, Spanish Ministry of Economy and Competitiveness, Comunidad Autonoma de Madrid, Medical Research Council (United Kingdom)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.203 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Literature

Deconvolution of Buparlisib's mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention.

Bohnacker, T., Prota, A.E., Beaufils, F., Burke, J.E., Melone, A., Inglis, A.J., Rageot, D., Sele, A.M., Cmiljanovic, V., Cmiljanovic, N., Bargsten, K., Aher, A., Akhmanova, A., Diaz, J.F., Fabbro, D., Zvelebil, M., Williams, R.L., Steinmetz, M.O., Wymann, M.P.

(2017) Nat Commun 8: 14683-14683

• PubMed: 28276440 
• DOI: 10.1038/ncomms14683
• Primary Citation of Related Structures:  
  5M8D, 5M8G, 5JHB, 5JHA, 5M7G, 5M7E


• PubMed Abstract: 
  

BKM120 (Buparlisib) is one of the most advanced phosphoinositide 3-kinase (PI3K) inhibitors for the treatment of cancer, but it interferes as an off-target effect with microtubule polymerization. Here, we developed two chemical derivatives that differ from BKM120 by only one atom. We show that these minute changes separate the dual activity of BKM120 into discrete PI3K and tubulin inhibitors. Analysis of the compounds cellular growth arrest phenotypes and microtubule dynamics suggest that the antiproliferative activity of BKM120 is mainly due to microtubule-dependent cytotoxicity rather than through inhibition of PI3K. Crystal structures of BKM120 and derivatives in complex with tubulin and PI3K provide insights into the selective mode of action of this class of drugs. Our results raise concerns over BKM120's generally accepted mode of action, and provide a unique mechanistic basis for next-generation PI3K inhibitors with improved safety profiles and flexibility for use in combination therapies.

---

Organizational Affiliation: 

Department of Biomedicine, University of Basel, 4058 Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Bos taurus	Mutation(s): 0
Find proteins for P81947 (Bos taurus) Explore P81947  Go to UniProtKB:  P81947

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	B, D	445	Bos taurus	Mutation(s): 0  Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Stathmin-4	E	143	Rattus norvegicus	Mutation(s): 0  Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus) Explore P63043  Go to UniProtKB:  P63043

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-Tyrosine Ligase	F	384	Gallus gallus	Mutation(s): 0  Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus) Explore E1BQ43  Go to UniProtKB:  E1BQ43

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	A, C	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP	F	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP	B, D	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
SD5	B	5-[2,6-di(morpholin-4-yl)pyrimidin-4-yl]-4-(trifluoromethyl)pyridin-2-amine C18 H21 F3 N6 O2 CWHUFRVAEUJCEF-UHFFFAOYSA-N
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	A, F	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A, B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A, B, C, D, F	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.203 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.593	α = 90
b = 157.985	β = 90
c = 179.728	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-27 
• Released Date: 2017-02-22 
Deposition Author(s): Bohnacker, T., Prota, A.E., Steinmetz, M.O., Wymann, M.P.

---

Funding Organization	Location	Grant Number
Swiss Commission for Technology and Innovation (CTI)	Switzerland	14032.1 ; 15811.2 ; 17241.1
Stiftung fuer Krebsbekaempfung	Switzerland	341
Swiss National Science Foundation	Switzerland	310030_153211 ; 316030_133860 ; 310030B_138659; 31003A_166608 ;
Spanish Ministry of Economy and Competitiveness	Spain	BIO2013-42984-R
Comunidad Autonoma de Madrid	Spain	S2010/BMD-2457 BIPEDD2
Medical Research Council (United Kingdom)	United Kingdom	U105184308

Revision History 

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references, Structure summary
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence