Structure of hPNMT with inhibitor 7-(N-4-chlorophenylaminosulfonyl)-THIQ and AdoHcy

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 

Starting Model: experimental
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Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase

Gee, C.L.Drinkwater, N.Tyndall, J.D.A.Grunewald, G.L.Wu, Q.McLeish, M.J.Martin, J.L.

(2007) J Med Chem 50: 4845-4853

  • DOI: https://doi.org/10.1021/jm0703385
  • Primary Citation of Related Structures:  
    2G70, 2G71, 2G72, 2OBF, 2ONY, 2ONZ, 2OPB

  • PubMed Abstract: 

    Shape complementarity is a fundamental principle of inhibitor design. Here we show that an enzyme for which the crystal structure has been determined (phenylethanolamine N-methyltransferase, PNMT) conceals a cryptic binding site. This site is revealed upon binding of inhibitors that are double the size of the physiological substrate. These large inhibitors are not predicted to bind in that they protrude through the accessible surface calculated from a PNMT/7-aminosulfonyl-1,2,3,4-tetrahydroisoquinoline (SK&F 29661) crystal structure, yet they are potent inhibitors of PNMT. We determined structures of the enzyme complexed with large inhibitors and found that the volume of the active site increases by 140 A3 upon binding. Changes in active site size and shape are brought about by unfavorable side chain conformations and rigid body helix motions. The energetic cost is modest, estimated at 2-3 kcal/mol from mutational analyses. Our findings further underline the importance of protein flexibility in structure-based inhibitor design studies.

  • Organizational Affiliation

    Institute for Molecular Bioscience and ARC Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane, Qld, 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 
UniProt & NIH Common Fund Data Resources
Find proteins for P11086 (Homo sapiens)
Explore P11086 
Go to UniProtKB:  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:  2ONY Ki: min: 1.40e+4, max: 6.23e+4 (nM) from 3 assay(s)
TMJ BindingDB:  2ONY Ki: min: 210, max: 3770 (nM) from 3 assay(s)
PDBBind:  2ONY Ki: 210 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.96α = 90
b = 93.96β = 90
c = 188.03γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description