2BY4 | pdb_00002by4

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

PDB DOI: https://doi.org/10.2210/pdb2BY4/pdb

Classification: HYDROLASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2005-07-28 Released: 2006-04-07
Deposition Author(s): Jensen, A.L., Moller, J.V., Soehoel, H., Denmeade, S.R., Isaacs, J.T., Olsen, C.E., Christensen, S.B., Nissen, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.314 (Depositor), 0.313 (DCC)
R-Value Work:
0.254 (Depositor), 0.252 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 16412648 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2005.12.001
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 111.06 kDa
Atom Count: 7,767
Modeled Residue Count: 994
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1	A	994	Oryctolagus cuniculus	Mutation(s): 0 EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191 Go to UniProtKB: P04191
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AD4 Query on AD4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.314 (Depositor), 0.313 (DCC)
R-Value Work: 0.254 (Depositor), 0.252 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.739	α = 90
b = 71.739	β = 90
c = 593.656	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-04-07

Deposition Author(s):

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
Version 1.4: 2024-11-06
Changes: Structure summary