5Y4H

Human SIRT3 in complex with halistanol sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report



Literature

Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria

Nakamura, F.Kudo, N.Tomachi, Y.Nakata, A.Takemoto, M.Ito, A.Tabei, H.Arai, D.de Voogd, N.Yoshida, M.Nakao, Y.Fusetani, N.

(2018) J Antibiot (Tokyo) 71: 273-278

  • DOI: 10.1038/ja.2017.145
  • Primary Citation of Related Structures:  
    5Y4H

  • PubMed Abstract: 
  • Two new analogs of halistanol sulfate (1) were isolated from a marine sponge Halichondria sp. collected at Hachijo-jima Island. Structures of these new halistanol sulfates I (2) and J (3) were elucidated by spectral analyses. Compounds 1-3 showed inhibit ...

    Two new analogs of halistanol sulfate (1) were isolated from a marine sponge Halichondria sp. collected at Hachijo-jima Island. Structures of these new halistanol sulfates I (2) and J (3) were elucidated by spectral analyses. Compounds 1-3 showed inhibitory activity against SIRT 1-3 with IC 50 ranges of 45.9-67.9, 18.9-21.1 and 21.8-37.5 μM, respectively. X-ray crystallography of the halistanol sulfate (1) and SIRT3 complex clearly indicates that 1 binds to the exosite of SIRT3 that we have discovered in this study.


    Related Citations: 
    • Correction to: Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria
      Nakamura, F., Kudo, N., Tomachi, Y., Nakata, A., Takemoto, M., Ito, A., Tabei, H., Arai, D., de Voogd, N., Yoshida, M., Nakao, Y., Fusetani, N.
      (2018) J Antibiot (Tokyo) 71: 483

    Organizational Affiliation

    Fisheries and Oceans Hakodate, Hakodate, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial A285Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
NIH Common Fund Data Resources
PHAROS:  Q9NTG7
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG B12Homo sapiensMutation(s): 0 
Gene Names: ACSS1ACAS2LKIAA1846
EC: 6.2.1.1 (UniProt), 6.2.1.17 (UniProt)
Find proteins for Q9NUB1 (Homo sapiens)
Explore Q9NUB1 
Go to UniProtKB:  Q9NUB1
NIH Common Fund Data Resources
PHAROS:  Q9NUB1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8QF
Query on 8QF

Download Ideal Coordinates CCD File 
A
[(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-6,6-dimethylheptan-2-yl]-10,13-dimethyl-2,3-disulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-6-yl] hydrogen sulfate
C28 H50 O12 S3
MNVNGGMQJFYHMK-NZLCMVQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
BL-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.84α = 90
b = 127.84β = 90
c = 127.84γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapanKAKENHI 26221204
JSPSJapanP-Direct

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release