4BHI

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 3-(1,1,1,2-Tetramethylhydrazin-1-ium-2-yl)propanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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)propano ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GAMMA-BUTYROBETAINE DIOXYGENASE
A
387Homo sapiensMutation(s): 0 
Gene Names: BBOX1 (BBH, BBOX)
EC: 1.14.11.1
Find proteins for O75936 (Homo sapiens)
Go to Gene View: BBOX1
Go to UniProtKB:  O75936
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
RUJ
Query on RUJ

Download SDF File 
Download CCD File 
A
3-(1,1,1,2-TETRAMETHYLHYDRAZIN-1-IUM-2-YL)PROPANOATE
C7 H17 N2 O2
NXHYIEABELXCMM-UHFFFAOYSA-O
 Ligand Interaction
16D
Query on 16D

Download SDF File 
Download CCD File 
A
HEXANE-1,6-DIAMINE
1,6-DIAMINOHEXANE
C6 H16 N2
NAQMVNRVTILPCV-UHFFFAOYSA-N
 Ligand Interaction
OGA
Query on OGA

Download SDF File 
Download CCD File 
A
N-OXALYLGLYCINE
C4 H5 N O5
BIMZLRFONYSTPT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RUJKd: 9300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.161 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 107.240α = 90.00
b = 107.240β = 90.00
c = 205.040γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-09
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection