4JHT

Crystal Structure of AlkB in complex with 5-carboxy-8-hydroxyquinoline (IOX1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.159 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.

Hopkinson, R.J.Tumber, A.Yapp, C.Chowdhury, R.Aik, W.Che, K.H.Li, X.S.Kristensen, J.B.L.King, O.N.F.Chan, M.C.Yeoh, K.K.Choi, H.Walport, L.J.Thinnes, C.C.Bush, J.T.Lejeune, C.Rydzik, A.M.Rose, N.R.Bagg, E.A.McDonough, M.A.Krojer, T.Yue, W.W.Ng, S.S.Olsen, L.Brennan, P.E.Oppermann, U.Muller-Knapp, S.Klose, R.J.Ratcliffe, P.J.Schofield, C.J.Kawamura, A.

(2013) Chem Sci 4: 3110-3117

  • DOI: https://doi.org/10.1039/C3SC51122G
  • Primary Citation of Related Structures:  
    4BIO, 4BIS, 4JHT

  • PubMed Abstract: 

    2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, N -oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and γ-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.


  • Organizational Affiliation

    Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase AlkB206Escherichia coli K-12Mutation(s): 0 
Gene Names: aidDalkBb2212JW2200
EC: 1.14.11.33
UniProt
Find proteins for P05050 (Escherichia coli (strain K12))
Explore P05050 
Go to UniProtKB:  P05050
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05050
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
8XQ PDBBind:  4JHT IC50: 1.02e+4 (nM) from 1 assay(s)
BindingDB:  4JHT IC50: 1.02e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.159 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.839α = 77.62
b = 38.848β = 75.01
c = 40.45γ = 66.1
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
GDAdata collection
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2014-09-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description