7VBX

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 20

• PDB DOI: https://doi.org/10.2210/pdb7VBX/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-09-01 Released: 2022-02-16 
• Deposition Author(s): Orita, T., Doi, S., Iwanaga, T., Fujishima, A., Adachi, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Literature

Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors.

Bessho, Y., Akaki, T., Hara, Y., Yamakawa, M., Obika, S., Mori, G., Ubukata, M., Yasue, K., Nakane, Y., Terasako, Y., Orita, T., Doi, S., Iwanaga, T., Fujishima, A., Adachi, T., Ueno, H., Motomura, T.

(2021) Bioorg Med Chem 52: 116514

• DOI: https://doi.org/10.1016/j.bmc.2021.116514

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.41 kDa 
• Atom Count: 2,858 
• Modelled Residue Count: 340 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	A	394	Homo sapiens	Mutation(s): 0  Gene Names: PDK2, PDHK2 EC: 2.7.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15119 (Homo sapiens) Explore Q15119  Go to UniProtKB:  Q15119
PHAROS:  Q15119 GTEx:  ENSG00000005882

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ZP (Subject of Investigation/LOI)	F [auth A]	(3~{S})-3-[5-(8-cyclopropyl-2-methyl-9~{H}-pyrido[2,3-b]indol-3-yl)-1,3,4-oxadiazol-2-yl]-4-methyl-~{N}-[(1~{R})-1-phenylethyl]pentanamide C31 H33 N5 O2 PHZKSLPIUQGPAT-KOSHJBKYSA-N
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.251 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.155	α = 90
b = 109.155	β = 90
c = 84.359	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
Coot	model building
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-16 
Deposition Author(s): Orita, T., Doi, S., Iwanaga, T., Fujishima, A., Adachi, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-02-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description