7NTR | pdb_00007ntr

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SUBSTRATE MIMIC 3-PHENYLPROPIONATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 
    0.241 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7NTR

Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 87.4 kDa 
  • Atom Count: 6,240 
  • Modeled Residue Count: 723 
  • Deposited Residue Count: 778 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase, cytosolic
A, B
389Homo sapiensMutation(s): 1 
Gene Names: BCAT1, BCT1, ECA39
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free:  0.241 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.844α = 90
b = 103.795β = 90
c = 110.158γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Released Date: 2022-09-21 
    • Deposition Author(s): Hillig, R.C.

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description