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 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 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) ...

    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

    Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-ketoglutarate-dependent dioxygenase AlkBA206Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8XQ
Query on 8XQ

Download Ideal Coordinates CCD File 
B [auth A]8-hydroxyquinoline-5-carboxylic acid
C10 H7 N O3
JGRPKOGHYBAVMW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8XQ PDBBind:  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