1YZ3

Structure of human pnmt complexed with cofactor product adohcy and inhibitor SK&F 64139


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural, mutagenic, and kinetic analysis of the binding of substrates and inhibitors of human phenylethanolamine N-methyltransferase

Wu, Q.Gee, C.L.Lin, F.Tyndall, J.D.Martin, J.L.Grunewald, G.L.McLeish, M.J.

(2005) J Med Chem 48: 7243-7252

  • DOI: 10.1021/jm050568o
  • Primary Citation of Related Structures:  
    1YZ3

  • PubMed Abstract: 
  • The X-ray structure of human phenylethanolamine N-methyltransferase (hPNMT) complexed with its product, S-adenosyl-L-homocysteine (4), and the most potent inhibitor reported to date, SK&F 64139 (7), was used to identify the residues involved in inhib ...

    The X-ray structure of human phenylethanolamine N-methyltransferase (hPNMT) complexed with its product, S-adenosyl-L-homocysteine (4), and the most potent inhibitor reported to date, SK&F 64139 (7), was used to identify the residues involved in inhibitor binding. Four of these residues, Val53, Lys57, Glu219 and Asp267, were replaced, in turn, with alanine. All variants had increased Km values for phenylethanolamine (10), but only D267A showed a noteworthy (20-fold) decrease in its kcat value. Both WT hPNMT and D267A had similar kcat values for a rigid analogue, anti-9-amino-6-(trifluoromethyl)benzonorbornene (12), suggesting that Asp267 plays an important role in positioning the substrate but does not participate directly in catalysis. The Ki values for the binding of inhibitors such as 7 to the E219A and D267A variants increased by 2-3 orders of magnitude. Further, the inhibitors were shown to bind up to 50-fold more tightly in the presence of S-adenosyl-L-methionine (3), suggesting that the binding of the latter brings about a conformational change in the enzyme.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, USA.



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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
SKA
Query on SKA

Download CCD File 
A, B
7,8-DICHLORO-1,2,3,4-TETRAHYDROISOQUINOLINE
C9 H9 Cl2 N
WFPUBEDBBOGGIQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SKAKi:  3   nM  BindingDB
SKAKi :  1.5499999523162842   nM  PDBBind
SKAIC50:  10000   nM  BindingDB
SKAIC50:  10   nM  BindingDB
SKAKi:  3.0999999046325684   nM  BindingDB
SKAIC50:  3   nM  BindingDB
SKAKi:  1.5499999523162842   nM  Binding MOAD
SAHKi:  29000   nM  BindingDB
SKAKi:  300   nM  BindingDB
SKAKi:  200   nM  BindingDB
SKAKi:  220   nM  BindingDB
SKAKi:  1.5499999523162842   nM  BindingDB
SKAKi:  240   nM  BindingDB
SKAKi:  1240   nM  BindingDB
SAHKi:  62300   nM  BindingDB
SKAKi:  3.0999999046325684   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.9α = 90
b = 93.9β = 90
c = 188.3γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
CNSrefinement
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description