2G72

Structure of hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholinosulfonamide-THIQ and AdoMet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1021/jm0703385
  • Primary Citation of Related Structures:  
    2G72, 2G71, 2G70, 2OBF, 2ONZ, 2ONY, 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 reveale ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phenylethanolamine N-methyltransferaseAB289Homo sapiensMutation(s): 0 
Gene Names: PNMTPENT
EC: 2.1.1.28
Find proteins for P11086 (Homo sapiens)
Explore P11086 
Go to UniProtKB:  P11086
NIH Common Fund Data Resources
PHAROS  P11086
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
F21
Query on F21

Download CCD File 
A, B
(3R)-3-(FLUOROMETHYL)-7-(THIOMORPHOLIN-4-YLSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE
C14 H19 F N2 O2 S2
SBUKSNPHYWXCDG-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
F21Ki :  315   nM  PDBBind
F21Ki:  315   nM  Binding MOAD
F21Ki:  1200   nM  BindingDB
F21Ki:  315   nM  BindingDB
F21Ki:  610   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.226 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.31α = 90
b = 94.31β = 90
c = 188.89γ = 90
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2007-10-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance