5NJH

Triazolopyrimidines stabilize microtubules by binding to the vinca inhibitor site of tubulin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

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Literature

Triazolopyrimidines Are Microtubule-Stabilizing Agents that Bind the Vinca Inhibitor Site of Tubulin.

Saez-Calvo, G., Sharma, A., Balaguer, F.A., Barasoain, I., Rodriguez-Salarichs, J., Olieric, N., Munoz-Hernandez, H., Berbis, M.A., Wendeborn, S., Penalva, M.A., Matesanz, R., Canales, A., Prota, A.E., Jimenez-Barbero, J., Andreu, J.M., Lamberth, C., Steinmetz, M.O., Diaz, J.F.

(2017) Cell Chem Biol 24: 737-750.e6

  • DOI: 10.1016/j.chembiol.2017.05.016
  • Primary Citation of Related Structures:  
    5NJH

  • PubMed Abstract: 

    • Microtubule-targeting agents (MTAs) are some of the clinically most successful anti-cancer drugs. Unfortunately, instances of multidrug resistances to MTA have been reported, which highlights the need for developing MTAs with different mechanistic properties ...

    Microtubule-targeting agents (MTAs) are some of the clinically most successful anti-cancer drugs. Unfortunately, instances of multidrug resistances to MTA have been reported, which highlights the need for developing MTAs with different mechanistic properties. One less explored class of MTAs are [1,2,4]triazolo[1,5-a]pyrimidines (TPs). These cytotoxic compounds are microtubule-stabilizing agents that inexplicably bind to vinblastine binding site on tubulin, which is typically targeted by microtubule-destabilizing agents. Here we used cellular, biochemical, and structural biology approaches to address this apparent discrepancy. Our results establish TPs as vinca-site microtubule-stabilizing agents that promote longitudinal tubulin contacts in microtubules, in contrast to classical microtubule-stabilizing agents that primarily promote lateral contacts. Additionally we observe that TPs studied here are not affected by p-glycoprotein overexpression, and suggest that TPs are promising ligands against multidrug-resistant cancer cells.

    Organizational Affiliation: 

    Department of Physical and Chemical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain. Electronic address: fer@cib.csic.es.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA, C450Bos taurusMutation(s): 0 
UniProt
Find proteins for P81947 (Bos taurus)
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Go to UniProtKB:  P81947
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UniProt GroupP81947
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chainB, D445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus)
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Go to UniProtKB:  Q6B856
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UniProt GroupQ6B856
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E143Rattus norvegicusMutation(s): 0 
Gene Names: Stmn4
UniProt
Find proteins for P63043 (Rattus norvegicus)
Explore P63043 
Go to UniProtKB:  P63043
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UniProt GroupP63043
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
tubulin tyrosine ligase TTLF384Gallus gallusMutation(s): 0 
Gene Names: TTL
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
G [auth A],
L [auth C]		GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ACP
Query on ACP
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Q [auth F]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N		 Ligand Interaction
GDP
Query on GDP
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I [auth B],
N [auth D]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
8Z8
Query on 8Z8
Download Ideal Coordinates CCD File 
K [auth B]5-chloranyl-7-[(1~{R},5~{S})-3-methoxy-8-azabicyclo[3.2.1]octan-8-yl]-6-[2,4,6-tris(fluoranyl)phenyl]-[1,2,4]triazolo[1,5-a]pyrimidine
C19 H17 Cl F3 N5 O
QLFREGOMFNYDON-GDNZZTSVSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
M [auth C],
O [auth D],
P [auth F]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8Z8 Binding MOAD:  5NJH Ka: 1.80e+5 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.43α = 90
b = 158.353β = 90
c = 173.458γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Database references