8F5F | pdb_00008f5f

human branched chain ketoacid dehydrogenase kinase in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.301 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.261 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8F5F

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 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.

Macromolecule Content 

  • Total Structure Weight: 90.36 kDa 
  • Atom Count: 5,289 
  • Modeled Residue Count: 644 
  • Deposited Residue Count: 776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
A, B
388Homo 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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
XGG
(Subject of Investigation/LOI)

Query on XGG



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
(2P)-2-[(4P)-4-{6-[(1-ethylcyclopropyl)methoxy]pyridin-3-yl}-1,3-thiazol-2-yl]benzoic acid
C21 H20 N2 O3 S
NMOXDKZFTLXESP-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.301 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.37α = 90
b = 118.37β = 90
c = 156.23γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
BUSTERphasing

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