2FQ6

Cystathionine beta-lyase (cbl) from escherichia coli in complex with n-hydrazinocarbonylmethyl-2-trifluoromethyl-benzamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


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:  
    2FQ6, 2GQN

  • 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 (CBL) against a library of 50 000 small molecules and have identified several compounds that inhibit CBL enzyme activity in vitro ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cystathionine beta-lyaseA, B415Escherichia coliMutation(s): 0 
Gene Names: metC
EC: 4.4.1.8 (PDB Primary Data), 4.4.1.13 (UniProt), 4.4.1.28 (UniProt)
UniProt
Find proteins for P06721 (Escherichia coli (strain K12))
Explore P06721 
Go to UniProtKB:  P06721
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06721
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P3F
Query on P3F
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		PHOSPHORIC ACID MONO-(5-HYDROXY-6-METHYL-4-{[2-(2-TRIFLUOROMETHYL-BENZOYLAMINO)-ACETYL]-HYDRAZONOMETHYL}-PYRIDIN-3-YLMETHYL)ESTER
C18 H18 F3 N4 O7 P
MCLYFEQPXXDFPI-HCBMXOAHSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
P3F PDBBind:  2FQ6 IC50: 79 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.83α = 90
b = 153.47β = 90
c = 151.45γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2006-01-17 
  • Released Date: 2006-12-26 
    • Deposition Author(s): Junop, M.S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance