4ZOL

Crystal Structure of Tubulin-Stathmin-TTL-Tubulysin M Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report



Literature

Structural Insights into the Pharmacophore of Vinca Domain Inhibitors of Microtubules

Wang, Y.Benz, F.W.Wu, Y.Wang, Q.Chen, Y.Chen, X.Li, H.Zhang, Y.Zhang, R.Yang, J.

(2016) Mol Pharmacol 89: 233-242

  • DOI: 10.1124/mol.115.100149
  • Primary Citation of Related Structures:  
    5BMV, 4ZI7, 4ZHQ, 4ZOL

  • PubMed Abstract: 
  • Antibody-drug conjugates (ADCs) have achieved great success in cancer therapy in recent years. Some peptidyl microtubule inhibitors consisting of natural and unnatural amino acids, such as monomethyl auristatin E (MMAE) and F (MMAF), are extremely cytoto ...

    Antibody-drug conjugates (ADCs) have achieved great success in cancer therapy in recent years. Some peptidyl microtubule inhibitors consisting of natural and unnatural amino acids, such as monomethyl auristatin E (MMAE) and F (MMAF), are extremely cytotoxic and have been used as a payload in ADCs. However, their precise molecular interaction with tubulin and microtubules remains unclear. We determined the crystal structures of tubulin in complex with three ultra-potent peptidyl microtubule inhibitors [MMAE, taltobulin (HTI- 286), and tubulysin M] at 2.5 Å. Our data showed that the three peptides bound to the vinca domain and shared a common and key pharmacophore containing two consecutive hydrophobic groups (Val, Ile-like side chain). These groups protruded in opposite directions into hydrophobic pockets on the tubulin β and α subunits. Nitrogen and oxygen atoms from the same backbone formed hydrogen bonds with Asn329 from the α subunit and Asp179 from the β subunit in a direction normal to the surface formed by the aforementioned hydrophobic groups. In addition, our crystal structure data indicated that tubulysin M bound to the β subunit alone, providing a structural explanation for its higher affinity. We also compared the conformations of two representative structurally different vinca domain compounds, ustiloxin D and vinblastine, with those of the aforementioned peptidyl ligands, and found that they shared a similar pharmacophore. Our findings lay a foundation for the rational design of novel vinca domain ligands and may facilitate the development of microtubule inhibitors with high specificity, affinity, and efficiency as payloads for ADCs in cancer therapy.


    Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China (Yu.W., Ya.W., Y.C., X.C., H.L., R.Z., J.Y.); Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Health Sciences Center, Louisville, Kentucky (F.W.B.); Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China (Q.W.); and Pharmacology and Pharmaceutical Sciences School of Medicine, Tsinghua University and Collaborative Innovation Center for Biotherapy, Beijing, China (Y.Z.) jinliangyang@scu.edu.cn rundongzhang@scu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chain AC451Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chain BD445Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4 E143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin-tyrosine ligase F384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Explore E1BQ43 
Go to UniProtKB:  E1BQ43
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
55Q
Query on 55Q

Download Ideal Coordinates CCD File 
B, D
(2R,4R)-4-{[(2-{(1R,3R)-1-(acetyloxy)-4-methyl-3-[methyl(N-{[(2S)-1-methylpiperidin-2-yl]carbonyl}-D-isoleucyl)amino]pentyl}-1,3-thiazol-4-yl)carbonyl]amino}-2-methyl-5-phenylpentanoic acid
C38 H57 N5 O7 S
POBZYODNVHQLFG-ZSNLZOIESA-N
 Ligand Interaction
GTP
Query on GTP

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

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F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
GDP
Query on GDP

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

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

Download Ideal Coordinates CCD File 
A, B, C, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.127α = 90
b = 154.824β = 90
c = 186.524γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-05-06 
  • Released Date: 2016-07-27 
  • Deposition Author(s): Wang, Y., Zhang, R.

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release