6AGK

The structure of CH-II-77-tubulin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Activity Relationship Study of Novel 6-Aryl-2-benzoyl-pyridines as Tubulin Polymerization Inhibitors with Potent Antiproliferative Properties.

Chen, H.Deng, S.Wang, Y.Albadari, N.Kumar, G.Ma, D.Li, W.White, S.W.Miller, D.D.Li, W.

(2020) J Med Chem 63: 827-846

  • DOI: 10.1021/acs.jmedchem.9b01815
  • Primary Citation of Related Structures:  
    6PC4, 6AGK

  • PubMed Abstract: 
  • We recently reported the crystal structure of tubulin in complex with a colchicine binding site inhibitor (CBSI), ABI-231, having 2-aryl-4-benzoyl-imidazole (ABI). Based on this and additional crystal structures, here we report the structure-activity ...

    We recently reported the crystal structure of tubulin in complex with a colchicine binding site inhibitor (CBSI), ABI-231, having 2-aryl-4-benzoyl-imidazole (ABI). Based on this and additional crystal structures, here we report the structure-activity relationship study of a novel series of pyridine analogues of ABI-231, with compound 4v being the most potent one (average IC 50 ∼ 1.8 nM) against a panel of cancer cell lines. We determined the crystal structures of another potent CBSI ABI-274 and 4v in complex with tubulin and confirmed their direct binding at the colchicine site. 4v inhibited tubulin polymerization, strongly suppressed A375 melanoma tumor growth, induced tumor necrosis, disrupted tumor angiogenesis, and led to tumor cell apoptosis in vivo. Collectively, these studies suggest that 4v represents a promising new generation of tubulin inhibitors.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy , University of Tennessee Health Science Center , Memphis , Tennessee 38163 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainAC450Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta-2B chainBD445Bos taurusMutation(s): 0 
Gene Names: TUBB2B
Find proteins for Q6B856 (Bos taurus)
Explore Q6B856 
Go to UniProtKB:  Q6B856
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Stathmin-4E143Rattus 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 ligaseF384Gallus gallusMutation(s): 0 
Gene Names: TTL
Find proteins for E1BQ43 (Gallus gallus)
Explore E1BQ43 
Go to UniProtKB:  E1BQ43
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
A, C, D
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

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B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
9WR
Query on 9WR

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B, D
[6-(3-hydroxy-4-methylphenyl)pyridin-2-yl](3,4,5-trimethoxyphenyl)methanone
C22 H21 N O5
BTWMVPMEPRQKQD-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.084α = 90
b = 157.062β = 90
c = 182.897γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references