5I5U

X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDRONAPHTHALENYL COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


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:  
    5I5Y, 5I5T, 5I5S, 5I5V, 5I5U, 5I5X, 5I5W, 5I60

  • 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 to BCATm, which were subsequently progressed to X-ray crystallography, where a number of exemplars showed significant diversity in their binding modes ...

    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

    Medicines Research Centre, GlaxoSmithKline R&D , Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase, mitochondrialA, B369Homo sapiensMutation(s): 0 
Gene Names: BCAT2BCATMBCT2ECA40
EC: 2.6.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O15382 (Homo sapiens)
Explore O15382 
Go to UniProtKB:  O15382
PHAROS:  O15382
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A], J [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
67Y (Subject of Investigation/LOI)
Query on 67Y

Download Ideal Coordinates CCD File 
D [auth A], K [auth B]2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide
C12 H15 N O2
BBTOVZWCAMQWRJ-LLVKDONJSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], L [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
67Y BindingDB:  5I5U IC50: 1.26e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.074α = 90
b = 105.995β = 90
c = 107.462γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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