3OZT

Rat catechol O-methyltransferase in complex with a catechol-type, 4-oxo-pyridinyl-containing inhibitor - humanized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Molecular Recognition at the Active Site of Catechol-O-methyltransferase (COMT): Adenine Replacements in Bisubstrate Inhibitors

Ellermann, M.Paulini, R.Jakob-Roetne, R.Lerner, C.Borroni, E.Roth, D.Ehler, A.Schweizer, W.B.Schlatter, D.Rudolph, M.G.Diederich, F.

(2011) Chemistry 17: 6369-6381

  • DOI: 10.1002/chem.201003648
  • Primary Citation of Related Structures:  3NW9, 3OE4, 3OE5, 3OZR, 3OZS

  • PubMed Abstract: 
  • L-Dopa, the standard therapeutic for Parkinson's disease, is inactivated by the enzyme catechol-O-methyltransferase (COMT). COMT catalyzes the transfer of an activated methyl group from S-adenosylmethionine (SAM) to its catechol substrates, such as L ...

    L-Dopa, the standard therapeutic for Parkinson's disease, is inactivated by the enzyme catechol-O-methyltransferase (COMT). COMT catalyzes the transfer of an activated methyl group from S-adenosylmethionine (SAM) to its catechol substrates, such as L-dopa, in the presence of magnesium ions. The molecular recognition properties of the SAM-binding site of COMT have been investigated only sparsely. Here, we explore this site by structural alterations of the adenine moiety of bisubstrate inhibitors. The molecular recognition of adenine is of special interest due to the great abundance and importance of this nucleobase in biological systems. Novel bisubstrate inhibitors with adenine replacements were developed by structure-based design and synthesized using a nucleosidation protocol introduced by Vorbrüggen and co-workers. Key interactions of the adenine moiety with COMT were measured with a radiochemical assay. Several bisubstrate inhibitors, most notably the adenine replacements thiopyridine, purine, N-methyladenine, and 6-methylpurine, displayed nanomolar IC(50) values (median inhibitory concentration) for COMT down to 6 nM. A series of six cocrystal structures of the bisubstrate inhibitors in ternary complexes with COMT and Mg(2+) confirm our predicted binding mode of the adenine replacements. The cocrystal structure of an inhibitor bearing no nucleobase can be regarded as an intermediate along the reaction coordinate of bisubstrate inhibitor binding to COMT. Our studies show that solvation varies with the type of adenine replacement, whereas among the adenine derivatives, the nitrogen atom at position 1 is essential for high affinity, while the exocyclic amino group is most efficiently substituted by a methyl group.


    Organizational Affiliation

    Laboratorium für Organische Chemie, ETH-Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catechol O-methyltransferase
A
221Rattus norvegicusGene Names: Comt
EC: 2.1.1.6
Find proteins for P22734 (Rattus norvegicus)
Go to UniProtKB:  P22734
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OZZ
Query on OZZ

Download SDF File 
Download CCD File 
A
N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-oxopyridin-1-yl)oxolan-2-yl]prop-2-enyl]-2,3-dihydroxy-5-nitro-benzamide
C19 H19 N3 O9
HVTOTCCLXQPREB-LDNIWRHMSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OZZIC50: 336000 nM BINDINGMOAD
OZZKi: 74900 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.905α = 90.00
b = 50.905β = 90.00
c = 168.198γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-23
    Type: Structure summary
  • Version 1.3: 2012-08-15
    Type: Structure summary
  • Version 1.4: 2017-11-08
    Type: Refinement description