3Q92 | pdb_00003q92

X-ray Structure of ketohexokinase in complex with a pyrimidopyrimidine analog 1

• PDB DOI: https://doi.org/10.2210/pdb3Q92/pdb

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


• Deposited: 2011-01-07 Released: 2012-01-18 
• Deposition Author(s): Abad, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.263 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Inhibitors of Ketohexokinase: Discovery of Pyrimidinopyrimidines with Specific Substitution that Complements the ATP-Binding Site.

Maryanoff, B.E., O'Neill, J.C., McComsey, D.F., Yabut, S.C., Luci, D.K., Jordan, A.D., Masucci, J.A., Jones, W.J., Abad, M.C., Gibbs, A.C., Petrounia, I.

(2011) ACS Med Chem Lett 2: 538-543

• PubMed: 24900346 
• DOI: https://doi.org/10.1021/ml200070g
• Primary Citation Related Structures: 
  3Q92, 3QA2, 3QAI


• PubMed Abstract: 
  

  Attenuation of fructose metabolism by the inhibition of ketohexokinase (KHK; fructokinase) should reduce body weight, free fatty acids, and triglycerides, thereby offering a novel approach to treat diabetes and obesity in response to modern diets. We have identified potent, selective inhibitors of human hepatic KHK within a series of pyrimidinopyrimidines (1). For example, 8, 38, and 47 exhibited KHK IC50 values of 12, 7, and 8 nM, respectively, and also showed potent cellular KHK inhibition (IC50 < 500 nM), which relates to their intrinsic potency vs KHK and their ability to penetrate cells. X-ray cocrystal structures of KHK complexes of 3, 8, and 47 revealed the important interactions within the enzyme's adenosine 5'-triphosphate (ATP)-binding pocket.

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Organizational Affiliation: 
• Johnson & Johnson Pharmaceutical Research & Development , Spring House, Pennsylvania 19477-0776, United States.

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: 69.29 kDa 
• Atom Count: 4,686 
• Modeled Residue Count: 597 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketohexokinase	A, B	313	Homo sapiens	Mutation(s): 0  Gene Names: KHK EC: 2.7.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P50053 (Homo sapiens) Explore P50053  Go to UniProtKB:  P50053
PHAROS:  P50053 GTEx:  ENSG00000138030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XNB	C [auth A], E [auth B]	N~8~-(cyclopropylmethyl)-N~4~-[2-(methylsulfanyl)phenyl]-2-(piperazin-1-yl)pyrimido[5,4-d]pyrimidine-4,8-diamine C21 H26 N8 S HFLMLZKGLUEWBU-UHFFFAOYSA-N
SO4	D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
XNB	BindingDB:  3Q92	IC50: min: 12, max: 500 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.263 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.88	α = 90
b = 86.073	β = 90
c = 136.65	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Abad, M.C.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description