7NY9 | pdb_00007ny9

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

PubMed: 36261130 Search on PubMedSearch on PubMed Central
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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54687
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UV5 (Subject of Investigation/LOI) Query on UV5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	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		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]