4BGM

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 3-Carboxy-N-(2-fluoroethyl)-N,N-dimethylpropan-1- aminium chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Targeting Carnitine Biosynthesis: Discovery of New Inhibitors Against Gamma-Butyrobetaine Hydroxylase.

Tars, K.Leitans, J.Kazaks, A.Zelencova, D.Liepinsh, E.Kuka, J.Makrecka, M.Lola, D.Andrianovs, V.Gustina, D.Grinberga, S.Liepinsh, E.Kalvinsh, I.Dambrova, M.Loza, E.Pugovics, O.

(2014) J Med Chem 57: 2213

  • DOI: https://doi.org/10.1021/jm401603e
  • Primary Citation of Related Structures:  
    4BG1, 4BGK, 4BGM, 4BHF, 4BHI, 4C5W

  • PubMed Abstract: 

    γ-Butyrobetaine hydroxylase (BBOX) catalyzes the conversion of gamma butyrobetaine (GBB) to l-carnitine, which is involved in the generation of metabolic energy from long-chain fatty acids. BBOX inhibitor 3-(1,1,1-trimethylhydrazin-1-ium-2-yl)propanoate (mildronate), which is an approved, clinically used cardioprotective drug, is a relatively poor BBOX inhibitor and requires high daily doses. In this paper we describe the design, synthesis, and properties of 51 compounds, which include both GBB and mildronate analogues. We have discovered novel BBOX inhibitors with improved IC50 values; the best examples are in the nanomolar range and about 2 orders of magnitude better when compared to mildronate. For six inhibitors, crystal structures in complex with BBOX have been solved to explain their activities and pave the way for further inhibitor design.


  • Organizational Affiliation

    Biomedical Research and Study Centre , Ratsupites 1, LV1067 Riga, Latvia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA-BUTYROBETAINE DIOXYGENASE387Homo sapiensMutation(s): 0 
EC: 1.14.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75936 (Homo sapiens)
Explore O75936 
Go to UniProtKB:  O75936
PHAROS:  O75936
GTEx:  ENSG00000129151 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75936
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.182α = 90
b = 107.182β = 90
c = 205.171γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description