7PJF

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent.

Gaillard, N.Sharma, A.Abbaali, I.Liu, T.Shilliday, F.Cook, A.D.Ehrhard, V.Bangera, M.Roberts, A.J.Moores, C.A.Morrissette, N.Steinmetz, M.O.

(2021) EMBO Mol Med 13: e13818-e13818

  • DOI: 10.15252/emmm.202013818
  • Primary Citation of Related Structures:  
    7PJE, 7PJF

  • PubMed Abstract: 
  • Infectious diseases caused by apicomplexan parasites remain a global public health threat. The presence of multiple ligand-binding sites in tubulin makes this protein an attractive target for anti-parasite drug discovery. However, despite remarkable successes as anti-cancer agents, the rational development of protozoan parasite-specific tubulin drugs has been hindered by a lack of structural and biochemical information on protozoan tubulins ...

    Infectious diseases caused by apicomplexan parasites remain a global public health threat. The presence of multiple ligand-binding sites in tubulin makes this protein an attractive target for anti-parasite drug discovery. However, despite remarkable successes as anti-cancer agents, the rational development of protozoan parasite-specific tubulin drugs has been hindered by a lack of structural and biochemical information on protozoan tubulins. Here, we present atomic structures for a protozoan tubulin and microtubule and delineate the architectures of apicomplexan tubulin drug-binding sites. Based on this information, we rationally designed the parasite-specific tubulin inhibitor parabulin and show that it inhibits growth of parasites while displaying no effects on human cells. Our work presents for the first time the rational design of a species-specific tubulin drug providing a framework to exploit structural differences between human and protozoa tubulin variants enabling the development of much-needed, novel parasite inhibitors.


    Organizational Affiliation

    Biozentrum University of Basel, Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA451Homo sapiensMutation(s): 0 
Gene Names: TUBA1B
UniProt & NIH Common Fund Data Resources
Find proteins for P68363 (Homo sapiens)
Explore P68363 
Go to UniProtKB:  P68363
PHAROS:  P68363
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68363
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-3 chainB450Homo sapiensMutation(s): 0 
Gene Names: TUBB3TUBB4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13509 (Homo sapiens)
Explore Q13509 
Go to UniProtKB:  Q13509
PHAROS:  Q13509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13509
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Designed ankyrin repeat protein (DARPIN) D1C [auth F]157synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.784α = 90
b = 91.312β = 97.55
c = 82.657γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novartis FreeNovationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.2: 2021-11-17
    Changes: Data collection, Database references