2BY4

SR Ca(2+)-ATPase in the HnE2 state complexed with the thapsigargin derivative Boc-12ADT.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Natural Products as Starting Materials for Development of Second-Generation Serca Inhibitors Targeted Towards Prostate Cancer Cells

Soehoel, H.Jensen, A.L.Moller, J.V.Nissen, P.Denmeade, S.R.Isaacs, J.T.Olsen, C.E.Christensen, S.B.

(2006) Bioorg Med Chem 14: 2810

  • DOI: https://doi.org/10.1016/j.bmc.2005.12.001
  • Primary Citation of Related Structures:  
    2BY4

  • PubMed Abstract: 

    An analysis of the binding of the 8-O-N-tert-butoxycarbonyl-12-aminododecanoyl derivative of 8-O-debutanoylthapsigargin to the target molecule, the SERCA pump, has revealed the importance of the length and flexibility of the side chain attached to O-8. Based on the analysis a series of analogues to the 2-unsubstituted analogue trilobolide has been constructed and shown to be equipotent with thapsigargin as SERCA inhibitors. Only the 12-Boc-aminododecaonoyl derivative, however, was found to be apoptotic.


  • Organizational Affiliation

    Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1994Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.3.8
Membrane Entity: Yes 
UniProt
Find proteins for P04191 (Oryctolagus cuniculus)
Explore P04191 
Go to UniProtKB:  P04191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AD4
Query on AD4

Download Ideal Coordinates CCD File 
B [auth A](3S,3AR,4S,6S,6AR,7S,8S,9BS)-6-(ACETYLOXY)-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-{[(2Z)-2-METHYLBUT-2-ENOYL]OXY}-7-(OCTANOYLOXY)-2-OXO-2,3,3A,4,5,6,6A,7,8,9B-DECAHYDROAZULENO[4,5-B]FURAN-4-YL 12-[(TERT-BUTOXYCARBONYL)AMINO]DODECANOATE
C47 H75 N O14
IBTNJSDBPZIGKM-GGGDSPQJSA-N
ACP
Query on ACP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.739α = 90
b = 71.739β = 90
c = 593.656γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-07
    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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description