2AOT

Histamine Methyltransferase Complexed with the Antihistamine Drug Diphenhydramine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for inhibition of histamine N-methyltransferase by diverse drugs

Horton, J.R.Sawada, K.Nishibori, M.Cheng, X.

(2005) J.Mol.Biol. 353: 334-344

  • DOI: 10.1016/j.jmb.2005.08.040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In mammals, histamine action is terminated through metabolic inactivation by histamine N-methyltransferase (HNMT) and diamine oxidase. In addition to three well-studied pharmacological functions, smooth muscle contraction, increased vascular permeabi ...

    In mammals, histamine action is terminated through metabolic inactivation by histamine N-methyltransferase (HNMT) and diamine oxidase. In addition to three well-studied pharmacological functions, smooth muscle contraction, increased vascular permeability, and stimulation of gastric acid secretion, histamine plays important roles in neurotransmission, immunomodulation, and regulation of cell proliferation. The histamine receptor H1 antagonist diphenhydramine, the antimalarial drug amodiaquine, the antifolate drug metoprine, and the anticholinesterase drug tacrine (an early drug for Alzheimer's disease) are surprisingly all potent HNMT inhibitors, having inhibition constants in the range of 10-100nM. We have determined the structural mode of interaction of these four inhibitors with HNMT. Despite their structural diversity, they all occupy the histamine-binding site, thus blocking access to the enzyme's active site. Near the N terminus of HNMT, several aromatic residues (Phe9, Tyr15, and Phe19) adopt different rotamer conformations or become disordered in the enzyme-inhibitor complexes, accommodating the diverse, rigid hydrophobic groups of the inhibitors. The maximized shape complementarity between the protein aromatic side-chains and aromatic ring(s) of the inhibitors are responsible for the tight binding of these varied inhibitors.


    Related Citations: 
    • Polymorphic Forms of Human Histamine Methyltransferase: Structural, Thermal, and Kinetic Comparisons
      Horton, J.R.,Sawada, K.,Nishibori, M.,Zhang, X.,Cheng, X.
      (2001) Structure 9: 837


    Organizational Affiliation

    Department of Biochemistry Emory University School of Medicine, 1510 Clifton Road Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histamine N-methyltransferase
A
292Homo sapiensMutation(s): 0 
Gene Names: HNMT
EC: 2.1.1.8
Find proteins for P50135 (Homo sapiens)
Go to Gene View: HNMT
Go to UniProtKB:  P50135
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histamine N-methyltransferase
B
292Homo sapiensMutation(s): 0 
Gene Names: HNMT
EC: 2.1.1.8
Find proteins for P50135 (Homo sapiens)
Go to Gene View: HNMT
Go to UniProtKB:  P50135
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
2PM
Query on 2PM

Download SDF File 
Download CCD File 
A, B
N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE
DIPHENHYDRAMINE, ANTISTOMINUM, BENZHYDRAMINE
C17 H21 N O
ZZVUWRFHKOJYTH-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHKi: 18100 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.221 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 131.670α = 90.00
b = 131.670β = 90.00
c = 63.750γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
GLRFphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance