5CR5

X-RAY CRYSTAL STRUCTURE AT 1.61A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIPHENYL PYRROLIDINE ETHER COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library.

Deng, H.Zhou, J.Sundersingh, F.S.Summerfield, J.Somers, D.Messer, J.A.Satz, A.L.Ancellin, N.Arico-Muendel, C.C.Sargent Bedard, K.L.Beljean, A.Belyanskaya, S.L.Bingham, R.Smith, S.E.Boursier, E.Carter, P.Centrella, P.A.Clark, M.A.Chung, C.W.Davie, C.P.Delorey, J.L.Ding, Y.Franklin, G.J.Grady, L.C.Herry, K.Hobbs, C.Kollmann, C.S.Morgan, B.A.Pothier Kaushansky, L.J.Zhou, Q.

(2015) Acs Med.Chem.Lett. 6: 919-924

  • DOI: 10.1021/acsmedchemlett.5b00179

  • PubMed Abstract: 
  • As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were di ...

    As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were discovered. One representative compound (R)-3-((1-(5-bromothiophene-2-carbonyl)pyrrolidin-3-yl)oxy)-N-methyl-2'-(methylsulfonamido)-[1,1'-biphenyl]-4-carboxamide (15e) from a novel compound library synthesized via on-DNA Suzuki-Miyaura cross-coupling showed BCATm inhibitory activity with IC50 = 2.0 μM. A protein crystal structure of 15e revealed that it binds to BCATm within the catalytic site adjacent to the PLP cofactor. The identification of this novel inhibitor series plus the establishment of a BCATm protein structure provided a good starting point for future structure-based discovery of BCATm inhibitors.


    Organizational Affiliation

    Platform Technology and Science, GlaxoSmithKline , 830 Winter Street, Waltham, Massachusetts 02451, United States.




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
EL1
Query on EL1

Download SDF File 
Download CCD File 
A, B
3-({(3R)-1-[(5-bromothiophen-2-yl)carbonyl]pyrrolidin-3-yl}oxy)-N-methyl-2'-[(methylsulfonyl)amino]biphenyl-4-carboxamide
C24 H24 Br N3 O5 S2
YDBFEELXWGATBW-MRXNPFEDSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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

Download SDF File 
Download CCD File 
B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-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 %)
EL1IC50: 2000 - 3900 nM (100) BINDINGDB
EL1IC50: 2000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.550α = 90.00
b = 105.590β = 90.00
c = 107.050γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-07-22 
  • Released Date: 2015-08-12 
  • Deposition Author(s): Somers, D.O.

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references