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

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1006/jmbi.2000.3607
  • Primary Citation of Related Structures:  
    1QIV, 1QIW

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
148Bos taurusMutation(s): 0 
Gene Names: CALMCAM
Find proteins for P62157 (Bos taurus)
Explore P62157 
Go to UniProtKB:  P62157
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62157
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DPD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B]
C34 H48 N2 O2
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
DPD Binding MOAD:  1QIW Kd: 18 (nM) from 1 assay(s)
PDBBind:  1QIW Kd: 18 (nM) from 1 assay(s)
BindingDB:  1QIW Kd: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.96α = 99.52
b = 56.2β = 114.47
c = 35.27γ = 96.86
Software Package:
Software NamePurpose
BIOTEXdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation