Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.77 kDa 
• Atom Count: 4326 
• Residue Count: 525 
• Unique protein chains: 1

3KQW

Crystal Structure of hPNMT in Complex AdoHcy and 5-Chlorobenzimidazole

• DOI: 10.2210/pdb3KQW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-17 Released: 2010-09-29 
• Deposition Author(s): Drinkwater, N., Martin, J.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

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

• PubMed: 20642456 
• DOI: 10.1042/BJ20100651
• Primary Citation of Related Structures:  
  3KPU, 3KPV, 3KPW, 3KPJ, 3KQQ, 3KR2, 3KQS, 3KQT, 3KQV, 3KQW


• 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylethanolamine N-methyltransferase	A, B	289	Homo sapiens	Mutation(s): 0  Gene Names: PNMT, PENT EC: 2.1.1.28
Find proteins for P11086 (Homo sapiens) Explore P11086  Go to UniProtKB:  P11086
NIH Common Fund Data Resources
PHAROS:  P11086 GTEx:  ENSG00000141744

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	A, B	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ES9	A, B	5-chloro-1H-benzimidazole C7 H5 Cl N2 NKLOLMQJDLMZRE-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAH	Ki:  62300   nM  BindingDB
ES9	Kd :  97000   nM  PDBBind
SAH	Ki:  29000   nM  BindingDB
ES9	Kd:  97000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.262 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.405	α = 90
b = 94.405	β = 90
c = 189.535	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MIFit	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-11-17 
• Released Date: 2010-09-29 
Deposition Author(s): Drinkwater, N., Martin, J.L.

Revision History 

• 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