4BG1

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 1-(3-Carboxypropyl)-1-methylpyrrolidin-1-ium chloride

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GAMMA-BUTYROBETAINE DIOXYGENASE A387Homo sapiensMutation(s): 0 
Gene Names: BBOX1, BBH, BBOX
EC: 1.14.11.1
Find proteins for O75936 (Homo sapiens)
Explore O75936 
Go to UniProtKB:  O75936
NIH Common Fund Data Resources
PHAROS:  O75936
GTEx:  ENSG00000129151
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IVL
Query on IVL
Download Ideal Coordinates CCD File 
A
1-(3-carboxypropyl)-1-methylpyrrolidin-1-ium
C9 H18 N O2
MXRVDXQFAGJLAO-UHFFFAOYSA-O		 Ligand Interaction
OGA
Query on OGA
Download Ideal Coordinates CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N		 Ligand Interaction
16D
Query on 16D
Download Ideal Coordinates CCD File 
A
HEXANE-1,6-DIAMINE
C6 H16 N2
NAQMVNRVTILPCV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IVLIC50:  490   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.63α = 90
b = 107.63β = 90
c = 205.53γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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