4ZI7

CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-HTI286 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  4ZHQ, 4ZOL, 5BMV

  • 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 cy ...

    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.).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C
451Sus scrofaGene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Go to Gene View: TUBA1B
Go to UniProtKB:  Q2XVP4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D
445Sus scrofaN/A
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Stathmin-4
E
143Rattus norvegicusGene Names: Stmn4
Find proteins for P63043 (Rattus norvegicus)
Go to UniProtKB:  P63043
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tubulin-Tyrosine Ligase
F
384Gallus gallusGene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Go to Gene View: TTL
Go to UniProtKB:  E1BQ43
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

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

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Download CCD File 
A, B, C, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
4SL
Query on 4SL

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Download CCD File 
B
N,beta,beta-trimethyl-L-phenylalanyl-N-[(3S,4Z)-5-carboxy-2-methylhex-4-en-3-yl]-N,3-dimethyl-L-valinamide
C27 H43 N3 O4
CNTMOLDWXSVYKD-ZUOPOVGWSA-N
 Ligand Interaction
MG
Query on MG

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A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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

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Download CCD File 
F
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002175 (4SL)
Query on PRD_002175
BN,beta,beta-trimethyl-L-phenylalanyl-N-[(3S,4Z)-5-carboxy-2-methylhex-4-en-3-yl]-N,3-dimethyl-L-valinamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 105.367α = 90.00
b = 157.343β = 90.00
c = 181.963γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-04-27 
  • Released Date: 2016-07-27 
  • Deposition Author(s): Wang, Y., Zhang, R.

Revision History 

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