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.

Macromolecule Content

• Total Structure Weight: 265.38 kDa 
• Atom Count: 17665 
• Modelled Residue Count: 2179 
• Deposited Residue Count: 2319 
• Unique protein chains: 4

5CA0

Crystal structure of T2R-TTL-Lexibulin complex

• DOI: 10.2210/pdb5CA0/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Sus scrofa, Rattus norvegicus, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-29 Released: 2015-11-04 
• Deposition Author(s): Wang, Y., Yu, Y., Chen, Q., Yang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery.

Wang, Y., Zhang, H., Gigant, B., Yu, Y., Wu, Y., Chen, X., Lai, Q., Yang, Z., Chen, Q., Yang, J.

(2016) FEBS J 283: 102-111

• PubMed: 26462166 
• DOI: 10.1111/febs.13555
• Primary Citation of Related Structures:  
  5C8Y, 5CA0, 5CA1, 5CB4


• PubMed Abstract: 
  

Microtubules are dynamic assemblies of αβ-tubulin heterodimers and have been recognized as highly attractive targets for cancer chemotherapy. A broad range of agents bind to tubulin and interfere with microtubule assembly. Despite having a long history of characterization, colchicine binding site inhibitors (CBSIs) have not yet reached the commercial phase as anti-cancer drugs to date. We determined the structures of tubulin complexed with a set of structurally diverse CBSIs (lexibulin, nocodazole, plinabulin and tivantinib), among which nocodazole and tivantinib are both binary-function inhibitors targeting cancer-related kinases and microtubules simultaneously. High resolution structures revealed the detailed interactions between these ligands and tubulin. Our results showed that the binding modes of the CBSIs were different from previous docking models, highlighting the importance of crystal structure information in structure-based drug design. A real structure-based pharmacophore was proposed to rationalize key common interactions of the CBSIs at the colchicine domain. Our studies provide a solid structural basis for developing new anti-cancer agents for the colchicine binding site.

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Organizational Affiliation: 

State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Sus scrofa	Mutation(s): 0  Gene Names: TUBA1B
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	B, D	445	Sus scrofa	Mutation(s): 0  Gene Names: TUBB
UniProt
Find proteins for F2Z5B2 (Sus scrofa) Explore F2Z5B2  Go to UniProtKB:  F2Z5B2

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	F	384	Gallus gallus	Mutation(s): 0  Gene Names: TTL
UniProt
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 (Subject of Investigation/LOI)	G [auth A], O [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP (Subject of Investigation/LOI)	T [auth F]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP (Subject of Investigation/LOI)	K [auth B], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
LXL (Subject of Investigation/LOI)	N [auth B], S [auth D]	1-ethyl-3-[2-methoxy-4-(5-methyl-4-{[(1S)-1-(pyridin-3-yl)butyl]amino}pyrimidin-2-yl)phenyl]urea C24 H30 N6 O2 MTJHLONVHHPNSI-IBGZPJMESA-N
MES	M [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	I [auth A], Q [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	H [auth A], L [auth B], P [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.06	α = 90
b = 158.444	β = 90
c = 181.825	γ = 90

Software Package:

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

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2015-06-29 
• Released Date: 2015-11-04 
Deposition Author(s): Wang, Y., Yu, Y., Chen, Q., Yang, J.

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references