1QIW

Calmodulin complexed with N-(3,3,-diphenylpropyl)-N'-[1-R-(3,4-bis-butoxyphenyl)-ethyl]-propylenediamine (DPD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A New Potent Calmodulin Antagonist with Arylalkylamine Structure: Crystallographic, Spectroscopic and Functional Studies

Harmat, V.Bocskei, Z.S.Naray-Szabo, G.Bata, I.Csutor, A.S.Hermecz, I.Aranyi, P.Szabo, B.Liliom, K.Vertessy, B.G.Ovadi, J.

(2000) J.Mol.Biol. 297: 747

  • DOI: 10.1006/jmbi.2000.3607
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • An arylalkylamine-type calmodulin antagonist, N-(3, 3-diphenylpropyl)-N'-[1-R-(3, 4-bis-butoxyphenyl)ethyl]-propylene-diamine (AAA) is presented and its complexes with calmodulin are characterized in solution and in the crystal. Near-UV circular dich ...

    An arylalkylamine-type calmodulin antagonist, N-(3, 3-diphenylpropyl)-N'-[1-R-(3, 4-bis-butoxyphenyl)ethyl]-propylene-diamine (AAA) is presented and its complexes with calmodulin are characterized in solution and in the crystal. Near-UV circular dichroism spectra show that AAA binds to calmodulin with 2:1 stoichiometry in a Ca(2+)-dependent manner. The crystal structure with 2:1 stoichiometry is determined to 2.64 A resolution. The binding of AAA causes domain closure of calmodulin similar to that obtained with trifluoperazine. Solution and crystal data indicate that each of the two AAA molecules anchors in the hydrophobic pockets of calmodulin, overlapping with two trifluoperazine sites, i.e. at a hydrophobic pocket and an interdomain site. The two AAA molecules also interact with each other by hydrophobic forces. A competition enzymatic assay has revealed that AAA inhibits calmodulin-activated phosphodiesterase activity at two orders of magnitude lower concentration than trifluoperazine. The apparent dissociation constant of AAA to calmodulin is 18 nM, which is commensurable with that of target peptides. On the basis of the crystal structure, we propose that the high-affinity binding is mainly due to a favorable entropy term, as the AAA molecule makes multiple contacts in its complex with calmodulin.


    Related Citations: 
    • Drug Binding by Calmodulin: Crystal Structure of a Calmodulin-Trifluoperazine Complex
      Cook, W.J.,Walter, L.J.,Walter, M.R.
      (1994) Biochemistry 33: 15259
    • Crystallization and Preliminary Diffraction Analysis of Ca(2+)-Calmodulin-Drug and Apocalmodulin-Drug Complexes.
      Vertessy, B.G.,Bocskei, Z.S.,Harmath, V.,Naray-Szabo, G.,Ovadi, J.
      (1997) Proteins: Struct.,Funct., Genet. 28: 131
    • Trifluoperazine-Induced Conformational Change in Ca (2+)-Calmodulin
      Vandonselaar, M.,Hickie, R.A.,Quail, J.W.,Delbaere, L.T.J.
      (1994) Nat.Struct.Mol.Biol. 1: 795


    Organizational Affiliation

    Department of Theoretical Chemistry, Loránd Eötvös University, Budapest 112, H-1518, Hungary. harmatv@ludens.elte.hu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CALMODULIN
A, B
148Bos taurusMutation(s): 0 
Gene Names: CALM (CAM)
Find proteins for P62157 (Bos taurus)
Go to UniProtKB:  P62157
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
DPD
Query on DPD

Download SDF File 
Download CCD File 
A, B
N-(3,3,-DIPHENYLPROPYL)-N'-[1-R-(2 3,4-BIS-BUTOXYPHENYL)-ETHYL]-PROPYLENEDIAMINE
C34 H48 N2 O2
VSFIKHFVWBEFKU-MUUNZHRXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DPDKd: 18 nM (100) BINDINGDB
DPDKd: 18 nM BINDINGMOAD
DPDKd: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.232 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.960α = 99.52
b = 56.200β = 114.47
c = 35.270γ = 96.86
Software Package:
Software NamePurpose
X-PLORphasing
BIOTEXdata reduction
X-PLORrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-07-05
    Type: Data collection