2AOU

Histamine Methyltransferase Complexed with the Antimalarial Drug Amodiaquine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 

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
  • Structures With Same Primary Citation

  • 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: 2
MoleculeChainsSequence LengthOrganismDetails
Histamine N-methyltransferase
B
292Homo sapiensMutation(s): 3 
Gene Names: HNMT
EC: 2.1.1.8
Find proteins for P50135 (Homo sapiens)
Go to UniProtKB:  P50135
NIH Common Fund Data Resources
PHAROS  P50135

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histamine N-methyltransferase
A
292Homo sapiensMutation(s): 3 
Gene Names: HNMT
EC: 2.1.1.8
Find proteins for P50135 (Homo sapiens)
Go to UniProtKB:  P50135
NIH Common Fund Data Resources
PHAROS  P50135
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CQA
Query on CQA

Download CCD File 
A, B
4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL
C20 H22 Cl N3 O
OVCDSSHSILBFBN-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 %)
CQAKi:  19   nM  BindingDB
CQAKi:  18.600000381469727   nM  Binding MOAD
CQAKi:  18.600000381469727   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.213 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.89α = 90
b = 130.89β = 90
c = 63.32γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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