4BR3

Determination of potential scaffolds for human choline kinase alpha 1 by chemical deconvolution studies

• PDB DOI: https://doi.org/10.2210/pdb4BR3/pdb

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


• Deposited: 2013-06-03 Released: 2013-06-19 
• Deposition Author(s): Sahun-Roncero, M., Rubio-Ruiz, B., Conejo-Garcia, A., Velazquez-Campoy, A., Entrena, A., Hurtado-Guerrero, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Determination of Potential Scaffolds for Human Choline Kinase Alpha 1 by Chemical Deconvolution Studies

Sahun-Roncero, M., Rubio-Ruiz, B., Conejo-Garcia, A., Velazquez-Campoy, A., Entrena, A., Hurtado-Guerrero, R.

(2013) Chembiochem 14: 1291

• PubMed: 23813777 
• DOI: https://doi.org/10.1002/cbic.201300195
• Primary Citation of Related Structures:  
  4BR3


• PubMed Abstract: 
  

  Dual binding modes: Combined empirical and computational studies of a series of compounds showed adenine and 1-benzyl-4-(dimethylamino)pyridinium fragments to function most efficiently in binding CHOKα1, and also determined how the latter fragment interacts with the choline binding site through two different binding modes. These data provide a basis for the future design of better and more selective inhibitors.

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Organizational Affiliation: 

Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.

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)

Macromolecule Content

• Total Structure Weight: 91.33 kDa 
• Atom Count: 6,147 
• Modelled Residue Count: 703 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHOLINE KINASE ALPHA	A, B	383	Homo sapiens	Mutation(s): 0  EC: 2.7.1.32 (PDB Primary Data), 2.7.1.82 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P35790 (Homo sapiens) Explore P35790  Go to UniProtKB:  P35790
PHAROS:  P35790 GTEx:  ENSG00000110721

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U85	C [auth A], E [auth B]	1-((4'-((6-amino-3H-purin-3-yl)methyl)biphenyl-4-yl)methyl)-4-(dimethylamino)pyridinium C26 H26 N7 YZNBHTPOBJOYMF-UHFFFAOYSA-N
A4V	D [auth A], F [auth B]	3-benzyladenine C12 H12 N5 SNSNPCORSVPUTC-UHFFFAOYSA-O
PO4	G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
U85	PDBBind:  4BR3	Kd: 1900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.258 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.737	α = 90
b = 122.254	β = 90
c = 132.173	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Sahun-Roncero, M., Rubio-Ruiz, B., Conejo-Garcia, A., Velazquez-Campoy, A., Entrena, A., Hurtado-Guerrero, R.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2013-07-31
  Changes: Database references
• Version 1.3: 2015-03-25
  Changes: Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description