7ZPE | pdb_00007zpe

human branched Chain Keto Acid Dehydrogenase Kinase in complex with ligand

• PDB DOI: https://doi.org/10.2210/pdb7ZPE/pdb

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


• Deposited: 2022-04-27 Released: 2025-11-12 
• Deposition Author(s): Kack, H., Wissler, L.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.255 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Combining druggability, co-evolution and rigidity analysis to map functional pockets

La Sala, G., Kack, H., Pfleger, C., Nevin, P., De vivo, M., Hogner, A., Tyrchan, C., Gohlke, H., Wissler, L., Frolov, A., Bohm, K., Janet, J.-P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 44.88 kDa 
• Atom Count: 2,526 
• Modeled Residue Count: 305 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain alpha-ketoacid dehydrogenase kinase	A	388	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JP6	G [auth A]	2-[(4-chlorophenyl)methylamino]-5-propyl-6~{H}-[1,2,4]triazolo[1,5-a]pyrimidin-7-one C15 H16 Cl N5 O ANNQZQCITGVRKA-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.255 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.594	α = 90
b = 129.594	β = 90
c = 73.215	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Kack, H., Wissler, L.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release