4BQX

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with Mn(II) and N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine (IOX3/UN9)

• PDB DOI: https://doi.org/10.2210/pdb4BQX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-03 Released: 2013-06-19 
• Deposition Author(s): Chowdhury, R., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.229 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.

Chowdhury, R., Candela-Lena, J.I., Chan, M.C., Greenald, D.J., Yeoh, K.K., Tian, Y.M., McDonough, M.A., Tumber, A., Rose, N.R., Conejo-Garcia, A., Demetriades, M., Mathavan, S., Kawamura, A., Lee, M.K., van Eeden, F., Pugh, C.W., Ratcliffe, P.J., Schofield, C.J.

(2013) ACS Chem Biol 8: 1488-1496

• PubMed: 23683440 
• DOI: https://doi.org/10.1021/cb400088q
• Primary Citation of Related Structures:  
  4BQW, 4BQX, 4BQY


• PubMed Abstract: 
  

  The hypoxia inducible factor (HIF) system is central to the signaling of low oxygen (hypoxia) in animals. The levels of HIF-α isoforms are regulated in an oxygen-dependent manner by the activity of the HIF prolyl-hydroxylases (PHD or EGLN enzymes), which are Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases. Here, we describe biochemical, crystallographic, cellular profiling, and animal studies on PHD inhibitors including selectivity studies using a representative set of human 2OG oxygenases. We identify suitable probe compounds for use in studies on the functional effects of PHD inhibition in cells and in animals.

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Organizational Affiliation: 

Department of Chemistry, Chemistry Research Laboratory, University of Oxford , Mansfield Road, Oxford, OX1 3TA, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.43 kDa 
• Atom Count: 1,861 
• Modelled Residue Count: 217 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EGL NINE HOMOLOG 1	A	252	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (PDB Primary Data), 1.14.11.29 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZT9 (Homo sapiens) Explore Q9GZT9  Go to UniProtKB:  Q9GZT9
PHAROS:  Q9GZT9 GTEx:  ENSG00000135766

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UN9	C [auth A]	N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE C12 H9 Cl N2 O4 OUQVKRKGTAUJQA-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
UN9	PDBBind:  4BQX	IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.229 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 109.6	β = 90
c = 39.33	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Chowdhury, R., Schofield, C.J.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 1.2: 2018-03-14
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.6: 2024-10-09
  Changes: Structure summary