6DE9

mitoNEET bound to furosemide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the mitochondrial protein mitoNEET bound to a benze-sulfonide ligand.

Geldenhuys, W.J.Long, T.E.Saralkar, P.Iwasaki, T.Nunez, R.A.A.Nair, R.R.Konkle, M.E.Menze, M.A.Pinti, M.V.Hollander, J.M.Hazlehurst, L.A.Robart, A.R.

(2019) Commun Chem 2

  • DOI: https://doi.org/10.1038/s42004-019-0172-x
  • Primary Citation of Related Structures:  
    6DE9

  • PubMed Abstract: 

    MitoNEET (gene cisd1 ) is a mitochondrial outer membrane [2Fe-2S] protein and is a potential drug target in several metabolic diseases. Previous studies have demonstrated that mitoNEET functions as a redox-active and pH-sensing protein that regulates mitochondrial metabolism, although the structural basis of the potential drug binding site(s) remains elusive. Here we report the crystal structure of the soluble domain of human mitoNEET with a sulfonamide ligand, furosemide. Exploration of the high-resolution crystal structure is used to design mitoNEET binding molecules in a pilot study of molecular probes for use in future development of mitochondrial targeted therapies for a wide variety of metabolic diseases, including obesity, diabetes and neurodegenerative diseases such as Alzheimer's and Parkinson's disease.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, School of Pharmacy West Virginia University, Morgantown, WV 26506, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CDGSH iron-sulfur domain-containing protein 178Homo sapiensMutation(s): 0 
Gene Names: CISD1C10orf70ZCD1MDS029
EC: 2.6.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ45 (Homo sapiens)
Explore Q9NZ45 
Go to UniProtKB:  Q9NZ45
PHAROS:  Q9NZ45
GTEx:  ENSG00000122873 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ45
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUN (Subject of Investigation/LOI)
Query on FUN

Download Ideal Coordinates CCD File 
C [auth A]5-(AMINOSULFONYL)-4-CHLORO-2-[(2-FURYLMETHYL)AMINO]BENZOIC ACID
C12 H11 Cl N2 O5 S
ZZUFCTLCJUWOSV-UHFFFAOYSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FUN BindingDB:  6DE9 Ki: 2285 (nM) from 1 assay(s)
Kd: 5.30e+4 (nM) from 1 assay(s)
IC50: min: 5.35e+4, max: 1.02e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.83α = 90
b = 58.83β = 90
c = 176.75γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2022-03-23
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Refinement description