7NY9

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 38

• PDB DOI: https://doi.org/10.2210/pdb7NY9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-03-22 Released: 2022-11-02 
• Deposition Author(s): Hillig, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Starting Model: experimental

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

• PubMed: 36261130 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 87.98 kDa 
• Atom Count: 6,803 
• Modelled Residue Count: 730 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Branched-chain-amino-acid aminotransferase, cytosolic	A, B	389	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UV5 (Subject of Investigation/LOI)	C [auth A], F [auth B]	3-[2,6-bis(oxidanylidene)-4-(trifluoromethyl)-5~{H}-pyrimidin-1-yl]-~{N}-methyl-2-pyridin-2-yl-imidazo[1,2-a]pyridine-7-carboxamide C19 H13 F3 N6 O3 QORQCYPXGXBYBR-UHFFFAOYSA-N
PLP	D [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.425	α = 90
b = 103.001	β = 90
c = 109.432	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
pointless	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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