8F5J

human branched chain ketoacid dehydrogenase kinase in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels.

Roth Flach, R.J.Bollinger, E.Reyes, A.R.Laforest, B.Kormos, B.L.Liu, S.Reese, M.R.Martinez Alsina, L.A.Buzon, L.Zhang, Y.Bechle, B.Rosado, A.Sahasrabudhe, P.V.Knafels, J.Bhattacharya, S.K.Omoto, K.Stansfield, J.C.Hurley, L.D.Song, L.Luo, L.Breitkopf, S.B.Monetti, M.Cunio, T.Tierney, B.Geoly, F.J.Delmore, J.Siddall, C.P.Xue, L.Yip, K.N.Kalgutkar, A.S.Miller, R.A.Zhang, B.B.Filipski, K.J.

(2023) Nat Commun 14: 4812-4812

  • DOI: https://doi.org/10.1038/s41467-023-40536-y
  • Primary Citation of Related Structures:  
    8F5F, 8F5J, 8F5S

  • PubMed Abstract: 

    Branched chain amino acid (BCAA) catabolic impairments have been implicated in several diseases. Branched chain ketoacid dehydrogenase (BCKDH) controls the rate limiting step in BCAA degradation, the activity of which is inhibited by BCKDH kinase (BDK)-mediated phosphorylation. Screening efforts to discover BDK inhibitors led to identification of thiophene PF-07208254, which improved cardiometabolic endpoints in mice. Structure-activity relationship studies led to identification of a thiazole series of BDK inhibitors; however, these inhibitors did not improve metabolism in mice upon chronic administration. While the thiophenes demonstrated sustained branched chain ketoacid (BCKA) lowering and reduced BDK protein levels, the thiazoles increased BCKAs and BDK protein levels. Thiazoles increased BDK proximity to BCKDH-E2, whereas thiophenes reduced BDK proximity to BCKDH-E2, which may promote BDK degradation. Thus, we describe two BDK inhibitor series that possess differing attributes regarding BDK degradation or stabilization and provide a mechanistic understanding of the desirable features of an effective BDK inhibitor.


  • Organizational Affiliation

    Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA. rachel.rothflach@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, mitochondrial388Homo sapiensMutation(s): 0 
Gene Names: BCKDK
EC: 2.7.11.4 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14874 (Homo sapiens)
Explore O14874 
Go to UniProtKB:  O14874
PHAROS:  O14874
GTEx:  ENSG00000103507 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14874
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.27α = 90
b = 132.27β = 90
c = 121.7γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-25
    Changes: Refinement description