2GQN

Cystathionine Beta-Lyase (CBL) from Escherichia Coli in complex with N-Hydrazinocarbonylmethyl-2-Nitro-Benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibitors of Bacterial Cystathionine beta-Lyase: Leads for New Antimicrobial Agents and Probes of Enzyme Structure and Function.

Ejim, L.J.Blanchard, J.E.Koteva, K.P.Sumerfield, R.Elowe, N.H.Chechetto, J.D.Brown, E.D.Junop, M.S.Wright, G.D.

(2007) J.Med.Chem. 50: 755-764

  • DOI: 10.1021/jm061132r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthesis of methionine is an attractive antibiotic target given its importance in protein and DNA metabolism and its absence in mammals. We have performed a high-throughput screen of the methionine biosynthesis enzyme cystathionine beta-lyase ...

    The biosynthesis of methionine is an attractive antibiotic target given its importance in protein and DNA metabolism and its absence in mammals. We have performed a high-throughput screen of the methionine biosynthesis enzyme cystathionine beta-lyase (CBL) against a library of 50 000 small molecules and have identified several compounds that inhibit CBL enzyme activity in vitro. These hit molecules were of two classes: those that blocked CBL activity with mixed steady-state inhibition and those that covalently interacted with the enzyme at the active site pyridoxal phosphate cofactor with slow-binding inhibition kinetics. We determined the crystal structure of one of the slow-binding inhibitors in complex with CBL and used this structure as a guide in the synthesis of a small, focused library of analogues, some of which had improved enzyme inhibition properties. These studies provide the first lead molecules for antimicrobial agents that target cystathionine beta-lyase in methionine biosynthesis.


    Organizational Affiliation

    Antimicrobial Research Centre, McMaster High Throughput Screening Laboratory, Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario L8N 3Z5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystathionine beta-lyase
A, B
415Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: metC
EC: 4.4.1.8
Find proteins for P06721 (Escherichia coli (strain K12))
Go to UniProtKB:  P06721
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BLP
Query on BLP

Download SDF File 
Download CCD File 
A, B
(5-HYDROXY-6-METHYL-4-((2-(2-(2-NITROBENZAMIDO)ACETYL)HYDRAZINYL)METHYL)PYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
C17 H20 N5 O9 P
AJHNLRARXNOGMZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BLPIC50: 4500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 59.637α = 90.00
b = 153.007β = 90.00
c = 151.240γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
CNSphasing
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance