8EGF

Branched chain ketoacid dehydrogenase kinase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural studies identify angiotensin II receptor blocker-like compounds as branched-chain ketoacid dehydrogenase kinase inhibitors.

Liu, S.Kormos, B.L.Knafels, J.D.Sahasrabudhe, P.V.Rosado, A.Sommese, R.F.Reyes, A.R.Ward, J.Roth Flach, R.J.Wang, X.Buzon, L.M.Reese, M.R.Bhattacharya, S.K.Omoto, K.Filipski, K.J.

(2023) J Biol Chem 299: 102959-102959

  • DOI: https://doi.org/10.1016/j.jbc.2023.102959
  • Primary Citation of Related Structures:  
    8EGD, 8EGF, 8EGQ, 8EGU

  • PubMed Abstract: 

    The mammalian mitochondrial branched-chain ketoacid dehydrogenase (BCKD) complex is a multienzyme complex involved in the catabolism of branched-chain amino acids. BCKD is regulated by the BCKD kinase, or BCKDK, which binds to the E2 subunit of BCKD, phosphorylates its E1 subunit, and inhibits enzymatic activity. Inhibition of the BCKD complex results in increased levels of branched-chain amino acids and branched-chain ketoacids, and this buildup has been associated with heart failure, type 2 diabetes mellitus, and nonalcoholic fatty liver disease. To find BCKDK inhibitors for potential treatment of these diseases, we performed both NMR and virtual fragment screening and identified tetrazole-bearing fragments that bind BCKDK at multiple sites. Through structure-based virtual screening expanding from these fragments, the angiotensin receptor blocker class antihypertension drugs and angiotensin receptor blocker-like compounds were discovered to be potent BCKDK inhibitors, suggesting potential new avenues for heart failure treatment combining BCKDK inhibition and antihypertension.


  • Organizational Affiliation

    Medicine Design, Pfizer Inc, Groton, Connecticut, USA. Electronic address: Shenping.liu@pfizer.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial388Rattus norvegicusMutation(s): 0 
Gene Names: Bckdk
EC: 2.7.11.4 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q00972 (Rattus norvegicus)
Explore Q00972 
Go to UniProtKB:  Q00972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00972
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
WIK (Subject of Investigation/LOI)
Query on WIK

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
(5P)-5-(4'-methyl[1,1'-biphenyl]-2-yl)-1H-tetrazole
C14 H12 N4
VWOJMXKARYCRCC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.401α = 90
b = 111.401β = 90
c = 140.547γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-03-08 
  • Deposition Author(s): Liu, S.

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description