Crystal Structure of hPNMT in Complex AdoHcy and Adenine

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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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: https://doi.org/10.1042/BJ20100651
  • Primary Citation of Related Structures:  
    3KPJ, 3KPU, 3KPV, 3KPW, 3KPY, 3KQM, 3KQO, 3KQP, 3KQQ, 3KQS, 3KQT, 3KQV, 3KQW, 3KQY, 3KR0, 3KR1, 3KR2

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phenylethanolamine N-methyltransferase
A, B
289Homo sapiensMutation(s): 0 
Gene Names: PNMTPENT
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens)
Explore P11086 
Go to UniProtKB:  P11086
PHAROS:  P11086
GTEx:  ENSG00000141744 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11086
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  3KPV Ki: min: 1.40e+4, max: 6.23e+4 (nM) from 3 assay(s)
ADE PDBBind:  3KPV Kd: 1.80e+5 (nM) from 1 assay(s)
Binding MOAD:  3KPV Kd: 1.80e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.178α = 90
b = 94.178β = 90
c = 188.801γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
JDirectordata collection
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description