4BN5

Structure of human SIRT3 in complex with SRT1720 inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Literature

Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and Srt1720: Binding Details and Inhibition Mechanism

Nguyen, G.T.T., Schaefer, S., Gertz, M., Weyand, M., Steegborn, C.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1423

  • DOI: 10.1107/S0907444913015448
  • Primary Citation of Related Structures:  
    4BN4, 4BN5

  • PubMed Abstract: 

    • Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging processes and are considered to be attractive therapeutic targets. Most available sirtuin modulators are little understood mechanistically, hindering their improvement. SRT1720 was initially described as an activator of human Sirt1, but it also potently inhibits human Sirt3 ...

    Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging processes and are considered to be attractive therapeutic targets. Most available sirtuin modulators are little understood mechanistically, hindering their improvement. SRT1720 was initially described as an activator of human Sirt1, but it also potently inhibits human Sirt3. Here, the molecular mechanism of the inhibition of Sirt3 by SRT1720 is described. A crystal structure of Sirt3 in complex with SRT1720 and an NAD(+) analogue reveals that the compound partially occupies the acetyl-Lys binding site, thus explaining the reported competition with the peptide substrate. The compound packs against a hydrophobic protein patch and binds with its opposite surface to the NAD(+)  nicotinamide, resulting in an exceptionally tight sandwich-like interaction. The observed arrangement rationalizes the uncompetitive inhibition with NAD(+), and binding measurements confirm that the nicotinamide moiety of NAD(+) supports inhibitor binding. Consistently, no inhibitor is bound in a second crystal structure of Sirt3 that was solved complexed with ADP-ribose and crystallized in the presence of SRT1720. These results reveal a novel sirtuin inhibitor binding site and mechanism, and provide a structural basis for compound improvement.

    Organizational Affiliation: 

    Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95445 Bayreuth, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
281Homo sapiensMutation(s): 0 
Gene Names: SIRT3, SIR2L3
EC: 3.5.1 (PDB Primary Data), 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNA
Query on CNA
Download Ideal Coordinates CCD File 
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
M [auth A],
AA [auth E],
DA [auth F],
GA [auth G],
JA [auth H],
M [auth A],
MA [auth I],
P [auth B],
PA [auth J],
S [auth C],
SA [auth K],
W [auth D],
WA [auth L]
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O		 Ligand Interaction
SR7
Query on SR7
Download Ideal Coordinates CCD File 
BA [auth E],
EA [auth F],
HA [auth G],
KA [auth H],
N [auth A],
BA [auth E],
EA [auth F],
HA [auth G],
KA [auth H],
N [auth A],
NA [auth I],
Q [auth B],
QA [auth J],
U [auth C],
UA [auth K],
Y [auth D],
YA [auth L]
N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide
C25 H23 N7 O S
IASPBORHOMBZMY-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
T [auth C],
TA [auth K],
X [auth D],
XA [auth L]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth E],
FA [auth F],
IA [auth G],
LA [auth H],
O [auth A],
CA [auth E],
FA [auth F],
IA [auth G],
LA [auth H],
O [auth A],
OA [auth I],
R [auth B],
RA [auth J],
V [auth C],
VA [auth K],
Z [auth D],
ZA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SR7 BindingDB:  4BN5 IC50: 850 (nM) from 1 assay(s)
EC50: 3.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 227.82α = 90
b = 246.06β = 123.88
c = 127.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2013-08-07
    Changes: Database references