2XH1

Crystal structure of human KAT II-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure-Based Selective Targeting of the Pyridoxal 5'-Phsosphate Dependent Enzyme Kynurenine Aminotransferase II for Cognitive Enhancement

Rossi, F.Casazza, V.Garavaglia, S.Sathyasaikumar, K.V.Schwarcz, R.Kojima, S.I.Okuwaki, K.Ono, S.I.Kajii, Y.Rizzi, M.

(2010) J Med Chem 53: 5684

  • DOI: https://doi.org/10.1021/jm100464k
  • Primary Citation of Related Structures:  
    2XH1

  • PubMed Abstract: 

    Fluctuations in the brain levels of the neuromodulator kynurenic acid may control cognitive processes and play a causative role in several catastrophic brain diseases. Elimination of the pyridoxal 5'-phosphate dependent enzyme kynurenine aminotransferase II reduces cerebral kynurenic acid synthesis and has procognitive effects. The present description of the crystal structure of human kynurenine aminotransferase II in complex with its potent and specific primary amine-bearing fluoroquinolone inhibitor (S)-(-)-9-(4-aminopiperazin-1-yl)-8-fluoro-3-methyl-6-oxo-2,3-dihydro-6H-1-oxa-3a-azaphenalene-5-carboxylic acid (BFF-122) should facilitate the structure-based development of cognition-enhancing drugs. From a medicinal chemistry perspective our results demonstrate that the issue of inhibitor specificity for highly conserved PLP-dependent enzymes could be successfully addressed.


  • Organizational Affiliation

    University of Piemonte Orientale Amedeo Avogadro, Novara, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
KYNURENINE/ALPHA-AMINOADIPATE AMINOTRANSFERASE, MITOCHONDRIAL
A, B
425Homo sapiensMutation(s): 1 
EC: 2.6.1.7 (PDB Primary Data), 2.6.1.39 (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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BF5
Query on BF5

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
(3S)-10-(4-AMINOPIPERAZIN-1-YL)-9-FLUORO-7-HYDROXY-3-METHYL-2,3-DIHYDRO-8H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLATE
C17 H19 F N4 O4
XSSSNYCVNIDBIB-VIFPVBQESA-M
PLP
Query on PLP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
IOD
Query on IOD

Download Ideal Coordinates CCD File 
E [auth A]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.323α = 90
b = 152.857β = 90
c = 60.8γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description