4C8R

Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Modulating carnitine levels by targeting its biosynthesis pathway - selective inhibition of gamma-butyrobetaine hydroxylase.

Rydzik, A.M.Chowdhury, R.Kochan, G.T.Williams, S.T.McDonough, M.A.Kawamura, A.Schofield, C.J.

(2014) Chem Sci 5: 1765-1771

  • DOI: https://doi.org/10.1039/C4SC00020J
  • Primary Citation of Related Structures:  
    4C8R

  • PubMed Abstract: 

    Carnitine is essential for fatty acid metabolism, but is associated with both health benefits and risks, especially heart diseases. We report the identification of potent, selective and cell active inhibitors of γ-butyrobetaine hydroxylase (BBOX), which catalyses the final step of carnitine biosynthesis in animals. A crystal structure of BBOX in complex with a lead inhibitor reveals that it binds in two modes, one of which adopts an unusual 'U-shape' conformation stabilised by inter- and intra-molecular π-stacking interactions. Conformational changes observed on binding of the inhibitor to BBOX likely reflect those occurring in catalysis; they also rationalise the inhibition of BBOX by high levels of its substrate γ-butyrobetaine (GBB), as observed both with isolated BBOX protein and in cellular studies.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAMMA-BUTYROBETAINE DIOXYGENASE
A, B, C, D, E
A, B, C, D, E, F
388Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6YT
Query on 6YT

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth E]
I [auth A]
JA [auth F]
O [auth B]
AA [auth D],
DA [auth E],
I [auth A],
JA [auth F],
O [auth B],
T [auth C]
N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine
C15 H15 N3 O4 S
KMBXCWNZAPWGKZ-NSHDSACASA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth E]
H [auth A]
IA [auth F]
N [auth B]
S [auth C]
CA [auth E],
H [auth A],
IA [auth F],
N [auth B],
S [auth C],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth E]
FA [auth E]
GA [auth E]
J [auth A]
K [auth A]
EA [auth E],
FA [auth E],
GA [auth E],
J [auth A],
K [auth A],
KA [auth F],
L [auth A],
LA [auth F],
P [auth B],
Q [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
BA [auth E]
G [auth A]
HA [auth F]
M [auth B]
R [auth C]
BA [auth E],
G [auth A],
HA [auth F],
M [auth B],
R [auth C],
Y [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.744α = 90
b = 91.659β = 90
c = 167.132γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Database references
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.3: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description