2ZDX

Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4.

Kukimoto-Niino, M.Tokmakov, A.Terada, T.Ohbayashi, N.Fujimoto, T.Gomi, S.Shiromizu, I.Kawamoto, M.Matsusue, T.Shirouzu, M.Yokoyama, S.

(2011) Acta Crystallogr.,Sect.D 67: 763-773

  • DOI: 10.1107/S090744491102405X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mitochondrial pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. PDC activity is tightly regulated by four members of a family of pyruvate dehydrogenase kinase isoforms (PDK1-4), which phosphor ...

    The mitochondrial pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. PDC activity is tightly regulated by four members of a family of pyruvate dehydrogenase kinase isoforms (PDK1-4), which phosphorylate and inactivate PDC. Recently, the development of specific inhibitors of PDK4 has become an especially important focus for the pharmaceutical management of diabetes and obesity. In this study, crystal structures of human PDK4 complexed with either AMPPNP, ADP or the inhibitor M77976 were determined. ADP-bound PDK4 has a slightly wider active-site cleft and a more disordered ATP lid compared with AMPPNP-bound PDK4, although both forms of PDK4 assume open conformations with a wider active-site cleft than that in the closed conformation of the previously reported ADP-bound PDK2 structure. M77976 binds to the ATP-binding pocket of PDK4 and causes local conformational changes with complete disordering of the ATP lid. M77976 binding also leads to a large domain rearrangement that further expands the active-site cleft of PDK4 compared with the ADP- and AMPPNP-bound forms. Biochemical analyses revealed that M77976 inhibits PDK4 with increased potency compared with the previously characterized PDK inhibitor radicicol. Thus, the present structures demonstrate for the first time the flexible and dynamic aspects of PDK4 in the open conformation and provide a basis for the development of novel inhibitors targeting the nucleotide-binding pocket of PDK4.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, Suehiro-cho, Tsurumi-ku, Yokohama, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate dehydrogenase kinase isozyme 4
A, B
394Homo sapiensMutation(s): 0 
Gene Names: PDK4 (PDHK4)
EC: 2.7.11.2
Find proteins for Q16654 (Homo sapiens)
Go to Gene View: PDK4
Go to UniProtKB:  Q16654
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4A
Query on P4A

Download SDF File 
Download CCD File 
A, B
4-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diol
3-(2,4-dihydroxyphenyl)-4-(4-methoxyphenyl)-5-methyl-1h-pyrazole
C17 H16 N2 O3
GSBFARPNIZUMHA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
P4AIC50: 648000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.083α = 90.00
b = 69.081β = 99.70
c = 85.627γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-23
    Type: Database references