4GE7 | pdb_00004ge7

Kynurenine Aminotransferase II Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4GE7

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • Pfizer Worldwide Research and Development , Neuroscience Medicinal Chemistry, Eastern Point Road, Groton, Connecticut 06340, United States.

Macromolecule Content 

  • Total Structure Weight: 98.93 kDa 
  • Atom Count: 7,390 
  • Modeled Residue Count: 856 
  • Deposited Residue Count: 878 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
A, B
439Homo sapiensMutation(s): 2 
Gene Names: AADATKAT2
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N5Z0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0K5

Query on 0K5



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
(5-hydroxy-4-{[(1-hydroxy-2-oxo-6-phenoxy-1,2-dihydroquinolin-3-yl)amino]methyl}-6-methylpyridin-3-yl)methyl dihydrogen phosphate
C23 H22 N3 O8 P
BVDVCYBTLXSYJB-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.74α = 90
b = 114.968β = 90
c = 116.548γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Structure summary