5BWW

X-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRROLIDINE AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 

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

    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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4W6
Query on 4W6

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Download CCD File 
A, B
7-oxo-2-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile
C16 H19 N5 O2
IBJDXQJWRXJZBH-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 
A, 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
DMS
Query on DMS

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Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

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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 %)
4W6IC50: 501 - <10000 nM (100) BINDINGDB
4W6IC50: 500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.290α = 90.00
b = 106.590β = 90.00
c = 106.810γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building

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