3KQW

Crystal Structure of hPNMT in Complex AdoHcy and 5-Chlorobenzimidazole

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.486 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors.

Drinkwater, N., Vu, H., Lovell, K.M., Criscione, K.R., Collins, B.M., Prisinzano, T.E., Poulsen, S.A., McLeish, M.J., Grunewald, G.L., Martin, J.L.

(2010) Biochem.J. 431: 51-61

  • DOI: 10.1042/BJ20100651
  • Primary Citation of Related Structures:  
  • Also Cited By: 4DM3

  • PubMed Abstract: 

    • CNS (central nervous system) adrenaline (epinephrine) is implicated in a wide range of physiological and pathological conditions. PNMT (phenylethanolamine N-methyltransferase) catalyses the final step in the biosynthesis of adrenaline, the conversion ...

    CNS (central nervous system) adrenaline (epinephrine) is implicated in a wide range of physiological and pathological conditions. PNMT (phenylethanolamine N-methyltransferase) catalyses the final step in the biosynthesis of adrenaline, the conversion of noradrenaline (norepinephrine) to adrenaline by methylation. To help elucidate the role of CNS adrenaline, and to develop potential drug leads, potent, selective and CNS-active inhibitors are required. The fragment screening approach has advantages over other lead discovery methods including high hit rates, more efficient hits and the ability to sample chemical diversity more easily. In the present study we applied fragment-based screening approaches to the enzyme PNMT. We used crystallography as the primary screen and identified 12 hits from a small commercial library of 384 drug-like fragments. The hits include nine chemicals with two fused rings and three single-ring chemical systems. Eight of the hits come from three chemical classes: benzimidazoles (a known class of PNMT inhibitor), purines and quinolines. Nine of the hits have measurable binding affinities (~5-700 μM) as determined by isothermal titration calorimetry and all nine have ligand efficiencies of 0.39 kcal/mol per heavy atom or better (1 kcal≈4.184 kJ). We synthesized five elaborated benzimidazole compounds and characterized their binding to PNMT, showing for the first time how this class of inhibitors interact with the noradrenaline-binding site. Finally, we performed a pilot study with PNMT for fragment-based screening by MS showing that this approach could be used as a fast and efficient first-pass screening method prior to characterization of binding mode and affinity of hits.

    Organizational Affiliation: 

    University of Queensland, Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, Brisbane, Queensland 4072, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phenylethanolamine N-methyltransferase
A, B
289Homo sapiensMutation(s): 0 
Gene Names: PNMT (PENT)
EC: 2.1.1.28
Find proteins for P11086 (Homo sapiens)
Go to Gene View: PNMT
Go to UniProtKB:  P11086
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ES9
Query on ES9
Download SDF File 
Download CCD File 
A, B
5-chloro-1H-benzimidazole
C7 H5 Cl N2
NKLOLMQJDLMZRE-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH
Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHKi: 29000 - 62300 nM (84) BINDINGDB
ES9Kd: 97000 nM BINDINGMOAD
ES9Kd: 97000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.486 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.194 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.405α = 90.00
b = 94.405β = 90.00
c = 189.535γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MIFitphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description