Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.13 kDa 
• Atom Count: 5623 
• Modelled Residue Count: 681 
• Deposited Residue Count: 788 
• Unique protein chains: 1

2ZDX

Inhibitor-bound structures of human pyruvate dehydrogenase kinase 4

• DOI: 10.2210/pdb2ZDX/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-11-30 Released: 2008-12-09 
• Deposition Author(s): Kawamoto, M., Shiromizu, I., Kukimoto-niino, M., Tokmakov, A., Terada, T., Shirouzu, M., Matsusue, T., Yokoyama, S.

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Experimental Data Snapshot

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

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 D Biol Crystallogr 67: 763-773

• PubMed: 21904029 
• DOI: 10.1107/S090744491102405X
• Primary Citation of Related Structures:  
  2E0A, 2ZDX, 2ZDY


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase kinase isozyme 4	A, B	394	Homo sapiens	Mutation(s): 0  Gene Names: PDK4, PDHK4 EC: 2.7.11.2
Find proteins for Q16654 (Homo sapiens) Explore Q16654  Go to UniProtKB:  Q16654
NIH Common Fund Data Resources
PHAROS:  Q16654 GTEx:  ENSG00000004799

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P4A	A, B	4-[4-(4-methoxyphenyl)-5-methyl-1H-pyrazol-3-yl]benzene-1,3-diol C17 H16 N2 O3 GSBFARPNIZUMHA-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
P4A	IC50 :  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 = 68.083	α = 90
b = 69.081	β = 99.7
c = 85.627	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-30 
• Released Date: 2008-12-09 
Deposition Author(s): Kawamoto, M., Shiromizu, I., Kukimoto-niino, M., Tokmakov, A., Terada, T., Shirouzu, M., Matsusue, T., Yokoyama, S.

Revision History  

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