6T8P | pdb_00006t8p

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: 2.02 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6T8P

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 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.

Macromolecule Content 

  • Total Structure Weight: 104.82 kDa 
  • Atom Count: 7,292 
  • Modeled Residue Count: 828 
  • Deposited Residue Count: 904 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial
A, B
452Homo sapiensMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MVT
(Subject of Investigation/LOI)

Query on MVT



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
J [auth B]
3,5-bis(fluoranyl)-~{N}-[5-[(2~{R})-2-(3-fluorophenyl)-3-methyl-butyl]-1,3,4-thiadiazol-2-yl]benzenesulfonamide
C19 H18 F3 N3 O2 S2
KRNZQAQFIHQJIO-QGZVFWFLSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO

Query on EDO



Download:Ideal Coordinates CCD File
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.057α = 90
b = 96.936β = 90
c = 116.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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, Refinement description