4FVT

Human SIRT3 bound to Ac-ACS peptide and Carba-NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 
    0.249 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CNAClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5.

Szczepankiewicz, B.G.Dai, H.Koppetsch, K.J.Qian, D.Jiang, F.Mao, C.Perni, R.B.

(2012) J Org Chem 77: 7319-7329

  • DOI: https://doi.org/10.1021/jo301067e
  • Primary Citation of Related Structures:  
    4FVT, 4G1C

  • PubMed Abstract: 

    Carba-NAD is a synthetic compound identical to NAD except for one substitution, where an oxygen atom adjacent to the anomeric linkage bearing nicotinamide is replaced with a methylene group. Because it is inert in nicotinamide displacement reactions, carba-NAD is an unreactive substrate analogue for NAD-consuming enzymes. SIRT3 and SIRT5 are NAD-consuming enzymes that are potential therapeutic targets for the treatment of metabolic diseases and cancers. We report an improved carba-NAD synthesis, including a pyrophosphate coupling method that proceeds in approximately 60% yield. We also disclose the X-ray crystal structures of the ternary complexes of SIRT3 and SIRT5 bound to a peptide substrate and carba-NAD. These X-ray crystal structures provide critical snapshots of the mechanism by which human sirtuins function as protein deacylation catalysts.


  • Organizational Affiliation

    Sirtris, a GSK Company, 200 Technology Square, Cambridge, Massachusetts 02139, USA. bruce.2.szczepankiewicz@gsk.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial274Homo sapiensMutation(s): 0 
EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
GTEx:  ENSG00000142082 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylated ACS2 peptide5N/AMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CNA
Query on CNA

Download Ideal Coordinates CCD File 
C [auth A]CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
Binding Affinity Annotations 
IDSourceBinding Affinity
CNA BindingDB:  4FVT Kd: min: 6600, max: 7300 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free:  0.249 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.43α = 90
b = 131.05β = 90
c = 77.32γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CNAClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2012-08-15 
  • Deposition Author(s): Dai, H.

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary