4GE4 | pdb_00004ge4

Kynurenine Aminotransferase II Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4GE4/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-08-01 Released: 2012-11-07 
• Deposition Author(s): Pandit, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Design of Irreversible Human KAT II Inhibitors: Discovery of New Potency-Enhancing Interactions.

Tuttle, J.B., Anderson, M., Bechle, B.M., Campbell, B.M., Chang, C., Dounay, A.B., Evrard, E., Fonseca, K.R., Gan, X., Ghosh, S., Horner, W., James, L.C., Kim, J.Y., McAllister, L.A., Pandit, J., Parikh, V.D., Rago, B.J., Salafia, M.A., Strick, C.A., Zawadzke, L.E., Verhoest, P.R.

(2013) ACS Med Chem Lett 4: 37-40

• PubMed: 24900560 
• DOI: https://doi.org/10.1021/ml300237v
• Primary Citation Related Structures: 
  4GE4, 4GE7, 4GE9


• PubMed Abstract: 
  

  A series of aryl hydroxamates recently have been disclosed as irreversible inhibitors of kynurenine amino transferase II (KAT II), an enzyme that may play a role in schizophrenia and other psychiatric and neurological disorders. The utilization of structure-activity relationships (SAR) in conjunction with X-ray crystallography led to the discovery of hydroxamate 4, a disubstituted analogue that has a significant potency enhancement due to a novel interaction with KAT II. The use of k inact/K i to assess potency was critical for understanding the SAR in this series and for identifying compounds with improved pharmacodynamic profiles.

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Organizational Affiliation: 
• Pfizer Worldwide Research and Development , Neuroscience Medicinal Chemistry, Eastern Point Road, Groton, Connecticut 06340, 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: 98.77 kDa 
• Atom Count: 6,965 
• Modeled Residue Count: 850 
• Deposited Residue Count: 878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial	A, B	439	Homo sapiens	Mutation(s): 2  Gene Names: AADAT, KAT2 EC: 2.6.1.39 (PDB Primary Data), 2.6.1.7 (PDB Primary Data), 2.6.1.4 (UniProt), 2.6.1.63 (UniProt), 2.6.1.73 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Z0 (Homo sapiens) Explore Q8N5Z0  Go to UniProtKB:  Q8N5Z0
PHAROS:  Q8N5Z0 GTEx:  ENSG00000109576

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0KE	C [auth A], D [auth B]	(5-hydroxy-4-{[(1-hydroxy-7-methoxy-2-oxo-1,2-dihydroquinolin-3-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate C18 H20 N3 O8 P QSKPSFPICSGYQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.944	α = 90
b = 111.944	β = 90
c = 137.508	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Pandit, J.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2014-07-16
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description