6T8Q

HKATII IN COMPLEX WITH LIGAND (2R)-N-benzyl-1-[6-methyl-5-(oxan-4-yl)-7-oxo-6H,7H-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]pyrrolidine-2-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of sulfonamides and 9-oxo-2,8-diazaspiro[5,5]undecane-2-carboxamides as human kynurenine aminotransferase 2 (KAT2) inhibitors.

Kalliokoski, T.Rummakko, P.Rantanen, M.Blaesse, M.Augustin, M.Ummenthala, G.R.Choudhary, S.Venalainen, J.

(2020) Bioorg Med Chem Lett 30: 127060-127060

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127060
  • Primary Citation of Related Structures:  
    6T8P, 6T8Q

  • PubMed Abstract: 

    Human kynurenine aminotransferase 2 (KAT2) inhibitors could be potentially used to treat the cognitive deficits associated with bipolar disease and schizophrenia. Although, there has been active drug research activity by several industrial and academic groups in developing KAT2 inhibitors over the years, no such compound has proceeded to the clinics. Here, we report two different chemical series of reversible KAT2 inhibitors with sub-micromolar activities. The first series was identified by a high-throughput screening of a diverse random library and the second one by structure-based virtual screening. Two novel crystal structures of KAT2 complexed with different reversible inhibitors were also deposited to the Protein databank which could be useful for future drug discovery efforts.


  • Organizational Affiliation

    Orion Pharma, Orionintie 1A, 02101 Espoo, Finland. Electronic address: tuomo.kalliokoski@orionpharma.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial452Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MVQ (Subject of Investigation/LOI)
Query on MVQ

Download Ideal Coordinates CCD File 
B [auth A](2~{R})-1-[6-methyl-5-(oxan-4-yl)-7-oxidanylidene-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]-~{N}-(phenylmethyl)pyrrolidine-2-carboxamide
C23 H27 N5 O3 S
FYUIPOUZYCBCCU-QGZVFWFLSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
L [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.829α = 90
b = 144.829β = 90
c = 139.653γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Database references
  • Version 1.2: 2020-03-18
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description