9DI9

Rat branched chain ketoacid dehydrogenase kinase in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of First Branched-Chain Ketoacid Dehydrogenase Kinase (BDK) Inhibitor Clinical Candidate PF-07328948.

Filipski, K.J.Martinez-Alsina, L.A.Reese, M.R.Evrard, E.Buzon, L.M.Cameron, K.O.Zhang, Y.Coffman, K.J.Bradow, J.Kormos, B.L.Liu, S.Knafels, J.D.Sahasrabudhe, P.V.Chen, J.Kalgutkar, A.S.Bessire, A.J.Orozco, C.C.Balesano, A.Cerny, M.A.Bollinger, E.Reyes, A.R.Laforest, B.Rosado, A.Williams, G.Marshall, M.Tam Neale, K.Chen, X.Hirenallur-Shanthappa, D.Stansfield, J.C.Groarke, J.Qiu, R.Karas, S.Roth Flach, R.J.Esler, W.P.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02230
  • Primary Citation of Related Structures:  
    9DI9

  • PubMed Abstract: 

    Inhibition of branched-chain ketoacid dehydrogenase kinase (BDK or BCKDK), a negative regulator of branched-chain amino acid (BCAA) metabolism, is hypothesized to treat cardio-metabolic diseases. From a starting point with potential idiosyncratic toxicity risk, modification to a benzothiophene core and discovery of a cryptic pocket allowed for improved potency with 3-aryl substitution to arrive at PF-07328948, which was largely devoid of protein covalent binding liability. This BDK inhibitor was shown also to be a BDK degrader in cells and in vivo rodent studies. Plasma biomarkers, including BCAAs and branched-chain ketoacids (BCKAs), were lowered in vivo with enhanced pharmacodynamic effect upon chronic dosing due to BDK degradation. This molecule improves metabolic and heart failure end points in rodent models. PF-07328948 is the first known selective BDK inhibitor candidate to be examined in clinical studies, with Phase 1 single ascending dose data showing good tolerability and a pharmacokinetic profile commensurate with once-daily dosing.


  • Organizational Affiliation

    Pfizer Research & Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain alpha-ketoacid dehydrogenase kinase388Homo sapiensMutation(s): 0 
Gene Names: BCKDK
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.4 (PDB Primary Data)
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 5 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
A1A40 (Subject of Investigation/LOI)
Query on A1A40

Download Ideal Coordinates CCD File 
E [auth A](3M)-6-fluoro-3-(2,4,5-trifluoro-3-methoxyphenyl)-1-benzothiophene-2-carboxylic acid
C16 H8 F4 O3 S
FXLDAQFHCAENIV-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.35α = 90
b = 126.35β = 90
c = 74.68γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-11-27 
  • Deposition Author(s): Liu, S.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references