5I5Y

X-RAY CRYSTAL STRUCTURE AT 1.81A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH AN ARYL ACETATE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening.

Borthwick, J.A.Ancellin, N.Bertrand, S.M.Bingham, R.P.Carter, P.S.Chung, C.W.Churcher, I.Dodic, N.Fournier, C.Francis, P.L.Hobbs, A.Jamieson, C.Pickett, S.D.Smith, S.E.Somers, D.O.Spitzfaden, C.Suckling, C.J.Young, R.J.

(2016) J.Med.Chem. 59: 2452-2467

  • DOI: 10.1021/acs.jmedchem.5b01607
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibitors of mitochondrial branched chain aminotransferase (BCATm), identified using fragment screening, are described. This was carried out using a combination of STD-NMR, thermal melt (Tm), and biochemical assays to identify compounds that bound t ...

    Inhibitors of mitochondrial branched chain aminotransferase (BCATm), identified using fragment screening, are described. This was carried out using a combination of STD-NMR, thermal melt (Tm), and biochemical assays to identify compounds that bound to BCATm, which were subsequently progressed to X-ray crystallography, where a number of exemplars showed significant diversity in their binding modes. The hits identified were supplemented by searching and screening of additional analogues, which enabled the gathering of further X-ray data where the original hits had not produced liganded structures. The fragment hits were optimized using structure-based design, with some transfer of information between series, which enabled the identification of ligand efficient lead molecules with micromolar levels of inhibition, cellular activity, and good solubility.


    Organizational Affiliation

    Les Ulis, Centre de Recherche, GlaxoSmithKline R&D , 25,27 Avenue du Qu├ębec, 91140 Villebon sur Yvette, France.,Medicines Research Centre, GlaxoSmithKline R&D , Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K.,Department of Pure and Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow, G1 1XL, 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
68D
Query on 68D

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Download CCD File 
A, B
{2-[(5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carbonyl)amino]phenyl}acetic acid
C16 H13 N3 O4 S
FLKHRDPJVSXBIP-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

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

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-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 %)
68DIC50: 1000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.150 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.920α = 90.00
b = 109.920β = 96.98
c = 59.918γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-15 
  • Released Date: 2016-03-23 
  • Deposition Author(s): Somers, D.O.

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-06
    Type: Database references