5BWV | pdb_00005bwv

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 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.5b00313
  • Primary Citation Related Structures: 
    5BWR, 5BWT, 5BWU, 5BWV, 5BWW, 5BWX

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 85.86 kDa 
  • Atom Count: 6,954 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 738 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Branched-chain-amino-acid aminotransferase, mitochondrial
A, B
369Homo sapiensMutation(s): 0 
Gene Names: BCAT2, BCATM, BCT2, ECA40
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
GTEx:  ENSG00000105552 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15382
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
775

Query on 775


Download:Ideal Coordinates CCD File
D [auth A],
U [auth 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
PLP

Query on PLP


Download:Ideal Coordinates CCD File
C [auth A],
T [auth B]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
GOL

Query on GOL


Download:Ideal Coordinates CCD File
S [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AA [auth B]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
AA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
V [auth B],
W [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
775 BindingDB:  5BWV IC50: min: 79, max: 631 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.211 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.57α = 90
b = 105.936β = 90
c = 108.03γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references, Structure summary