7NY2

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe.

Gunther, J.Hillig, R.C.Zimmermann, K.Kaulfuss, S.Lemos, C.Nguyen, D.Rehwinkel, H.Habgood, M.Lechner, C.Neuhaus, R.Ganzer, U.Drewes, M.Chai, J.Bouche, L.

(2022) J Med Chem 65: 14366-14390

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00441
  • Primary Citation of Related Structures:  
    7NTR, 7NWA, 7NWB, 7NWC, 7NWE, 7NWM, 7NXN, 7NXO, 7NY2, 7NY9, 7NYA

  • PubMed Abstract: 

    The branched-chain amino acid transaminases (BCATs) are enzymes that catalyze the first reaction of catabolism of the essential branched-chain amino acids to branched-chain keto acids to form glutamate. They are known to play a key role in different cancer types. Here, we report a new structural class of BCAT1/2 inhibitors, (trifluoromethyl)pyrimidinediones, identified by a high-throughput screening campaign and subsequent optimization guided by a series of X-ray crystal structures. Our potent dual BCAT1/2 inhibitor BAY-069 displays high cellular activity and very good selectivity. Along with a negative control (BAY-771), BAY-069 was donated as a chemical probe to the Structural Genomics Consortium.


  • Organizational Affiliation

    Research & Development, Pharmaceuticals, Bayer Pharma AG, Müllerstrasse 178, 13353Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase, cytosolic
A, B
389Homo sapiensMutation(s): 1 
Gene Names: BCAT1BCT1ECA39
EC: 2.6.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for P54687 (Homo sapiens)
Explore P54687 
Go to UniProtKB:  P54687
PHAROS:  P54687
GTEx:  ENSG00000060982 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54687
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UUQ BindingDB:  7NY2 IC50: min: 70, max: 90 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.459α = 90
b = 104.964β = 90
c = 110.693γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
pointlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2022-11-02 
  • Deposition Author(s): Hillig, R.C.

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description