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X-RAY CRYSTAL STRUCTURE AT 1.86A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits.

Bertrand, S.M.Ancellin, N.Beaufils, B.Bingham, R.P.Borthwick, J.A.Boullay, A.B.Boursier, E.Carter, P.S.Chung, C.W.Churcher, I.Dodic, N.Fouchet, M.H.Fournier, C.Francis, P.L.Gummer, L.A.Herry, K.Hobbs, A.Hobbs, C.I.Homes, P.Jamieson, C.Nicodeme, E.Pickett, S.D.Reid, I.H.Simpson, G.L.Sloan, L.A.Smith, S.E.Somers, D.O.Spitzfaden, C.Suckling, C.J.Valko, K.Washio, Y.Young, R.J.

(2015) J.Med.Chem. 58: 7140-7163

  • DOI: 10.1021/acs.jmedchem.5b00313
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The hybridization of hits, identified by complementary fragment and high throughput screens, enabled the discovery of the first series of potent inhibitors of mitochondrial branched-chain aminotransferase (BCATm) based on a 2-benzylamino-pyrazolo[1,5 ...

    The hybridization of hits, identified by complementary fragment and high throughput screens, enabled the discovery of the first series of potent inhibitors of mitochondrial branched-chain aminotransferase (BCATm) based on a 2-benzylamino-pyrazolo[1,5-a]pyrimidinone-3-carbonitrile template. Structure-guided growth enabled rapid optimization of potency with maintenance of ligand efficiency, while the focus on physicochemical properties delivered compounds with excellent pharmacokinetic exposure that enabled a proof of concept experiment in mice. Oral administration of 2-((4-chloro-2,6-difluorobenzyl)amino)-7-oxo-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile 61 significantly raised the circulating levels of the branched-chain amino acids leucine, isoleucine, and valine in this acute study.


    Organizational Affiliation

    Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow, G1 1XL, U.K.,Centre de Recherche, GlaxoSmithKline R&D, Les Ulis , 25, 27 Avenue du Qu├ębec, 91140 Villebon sur Yvette, France.,GlaxoSmithKline R&D, Medicines Research Centre , Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Branched-chain-amino-acid aminotransferase, mitochondrial
A, B
369Homo sapiensMutation(s): 0 
Gene Names: BCAT2 (BCATM, BCT2, ECA40)
EC: 2.6.1.42
Find proteins for O15382 (Homo sapiens)
Go to Gene View: BCAT2
Go to UniProtKB:  O15382
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
775
Query on 775

Download SDF File 
Download CCD File 
A, B
2-[(4-chlorobenzyl)amino]-7-oxo-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
C17 H16 Cl N5 O
WMUCQGGTSRVMIG-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
775IC50: 79 - 631 nM (100) BINDINGDB
775IC50: 79 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.570α = 90.00
b = 105.936β = 90.00
c = 108.030γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-08 
  • Released Date: 2015-07-01 
  • Deposition Author(s): Somers, D.O.

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-10-07
    Type: Database references
  • Version 1.2: 2019-06-12
    Type: Data collection, Structure summary