4BIO | pdb_00004bio

FACTOR INHIBITING HIF-1 ALPHA IN COMPLEX WITH 8-HYDROXYQUINOLINE-5- CARBOXYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.234 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4BIO

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 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.

Macromolecule Content 

  • Total Structure Weight: 41.7 kDa 
  • Atom Count: 2,946 
  • Modeled Residue Count: 339 
  • Deposited Residue Count: 352 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYPOXIA-INDUCIBLE FACTOR 1-ALPHA INHIBITOR352Homo sapiensMutation(s): 0 
EC: 1.14.11.30 (PDB Primary Data), 1.14.11.16 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT6 (Homo sapiens)
Explore Q9NWT6 
Go to UniProtKB:  Q9NWT6
PHAROS:  Q9NWT6
GTEx:  ENSG00000166135 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NWT6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8XQ

Query on 8XQ



Download:Ideal Coordinates CCD File
C [auth A]8-hydroxyquinoline-5-carboxylic acid
C10 H7 N O3
JGRPKOGHYBAVMW-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.234 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.72α = 90
b = 86.72β = 90
c = 147.23γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Other
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description