Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39982.77 
• Atom Count: 2738 
• Residue Count: 335 
• Unique protein chains: 1

3KCX

Factor inhibiting HIF-1 alpha in complex with Clioquinol

• DOI: 10.2210/pdb3KCX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2009-10-22 Released: 2010-04-28 
• Deposition Author(s): Moon, H., Han, S., Choe, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.292 
• R-Value Work: 0.244 

Literature

Crystal structures of human FIH-1 in complex with quinol family inhibitors

Moon, H., Han, S., Park, H., Choe, J.

(2010) Mol.Cells 29: 471-474

• PubMed: 20396966 
• DOI: 10.1007/s10059-010-0058-3
• Primary Citation of Related Structures:  
  3KCY


• PubMed Abstract: 
  

Hypoxia-Inducible Factor-1 (HIF-1) plays an important role as a transcription factor under hypoxia. It activates numerous genes including those involved in angiogenesis, glucose metabolisms, cell proliferation and cell survival. The HIF-1 alpha subunit is regulated by 2-oxoglutarate (OG)- and Fe(II)-dependent hydroxylases, including Factor Inhibiting HIF-1 (FIH-1). FIH-1 hydroxylates Asn803 of HIF-1 alpha and blocks its interaction with co-activating molecules. Quinol family compounds such as 5-chloro-7-iodo-8-hydroxyquinoline (Clioquinol) have been shown to inhibit the hydroxylation activity of FIH-1. Here we determined the complex crystal structures of FIH-1: Clioquinol and FIH-1: 8-Hydroxyquinoline. Clioquinol and 8-Hydroxyquinoline bind to the active site of FIH-1 by coordinating the Fe(II) ion, thereby inhibiting the binding of a co-substrate, 2OG. Contrary to other known FIH-1 inhibitors that have negative charges, Clioquinol and 8-hydroxyquinoline are neutral in charge and can provide a template for improved inhibitor design that can selectively inhibit FIH-1.

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Organizational Affiliation: 

Department of Life Science, University of Seoul, Seoul 130-743, Korea.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hypoxia-inducible factor 1-alpha inhibitor	A	335	Homo sapiens	Mutation(s): 0  Gene Names: HIF1AN (FIH1) EC: 1.14.11.30, 1.14.11.n4
Find proteins for Q9NWT6 (Homo sapiens) Go to Gene View: HIF1AN Go to UniProtKB:  Q9NWT6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CQL	A	5-chloro-7-iodoquinolin-8-ol Clioquinol C9 H5 Cl I N O QCDFBFJGMNKBDO-UHFFFAOYSA-N
FE2	A	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.292 
• R-Value Work: 0.244 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 86.746	α = 90.00
b = 86.746	β = 90.00
c = 146.525	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-22 
• Released Date: 2010-04-28 
• Deposition Author(s): Moon, H., Han, S., Choe, J.

Revision History 

• Version 1.0: 2010-04-28
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-02-26
  Type: Database references
• Version 1.3: 2017-11-01
  Type: Refinement description