Crystal structure of an Anticalin-colchicine complex

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 

Starting Model: experimental
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An engineered lipocalin that tightly complexes the plant poison colchicine for use as antidote and in bioanalytical applications.

Barkovskiy, M.Ilyukhina, E.Dauner, M.Eichinger, A.Skerra, A.

(2019) Biol Chem 400: 351-366

  • DOI: https://doi.org/10.1515/hsz-2018-0342
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Colchicine is a toxic alkaloid prevalent in autumn crocus (Colchicum autumnale) that binds to tubulin and inhibits polymerization of microtubules. Using combinatorial and rational protein design, we have developed an artificial binding protein based on the human lipocalin 2 that binds colchicine with a dissociation constant of 120 pm, i.e. 10000-fold stronger than tubulin. Crystallographic analysis of the engineered lipocalin, dubbed Colchicalin, revealed major structural changes in the flexible loop region that forms the ligand pocket at the open end of the eight-stranded β-barrel, resulting in a lid-like structure over the deeply buried colchicine. A cis-peptide bond between residues Phe71 and Pro72 in loop #2 constitutes a peculiar feature and allows intimate contact with the tricyclic ligand. Using directed evolution, we achieved an extraordinary dissociation half-life of more than 9 h for the Colchicalin-colchicine complex. Together with the chemical robustness of colchicine and availability of activated derivatives, this also opens applications as a general-purpose affinity reagent, including facile quantification of colchicine in biological samples. Given that engineered lipocalins, also known as Anticalin® proteins, represent a class of clinically validated biopharmaceuticals, Colchicalin may offer a therapeutic antidote to scavenge colchicine and reverse its poisoning effect in situations of acute intoxication.

  • Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising (Weihenstephan), Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalin174Homo sapiensMutation(s): 24 
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
GTEx:  ENSG00000148346 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80188
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LOC

Download Ideal Coordinates CCD File 
B [auth A]N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
C22 H25 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.201 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.68α = 90
b = 46.68β = 90
c = 136.85γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Helmholtz-Zentrum BerlinGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description