4JSR

Crystal Structure of human SIRT3 with ELT inhibitor 11c [N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Literature

Discovery of Thieno[3,2-d]pyrimidine-6-carboxamides as Potent Inhibitors of SIRT1, SIRT2, and SIRT3.

Disch, J.S., Evindar, G., Chiu, C.H., Blum, C.A., Dai, H., Jin, L., Schuman, E., Lind, K.E., Belyanskaya, S.L., Deng, J., Coppo, F., Aquilani, L., Graybill, T.L., Cuozzo, J.W., Lavu, S., Mao, C., Vlasuk, G.P., Perni, R.B.

(2013) J Med Chem 56: 3666-3679

  • DOI: 10.1021/jm400204k
  • Primary Citation of Related Structures:  
    4JSR, 4JT8, 4JT9

  • PubMed Abstract: 

    • The sirtuins SIRT1, SIRT2, and SIRT3 are NAD(+) dependent deacetylases that are considered potential targets for metabolic, inflammatory, oncologic, and neurodegenerative disorders. Encoded library technology (ELT) was used to affinity screen a 1.2 million heterocycle enriched library of DNA encoded small molecules, which identified pan-inhibitors of SIRT1/2/3 with nanomolar potency (e ...

    The sirtuins SIRT1, SIRT2, and SIRT3 are NAD(+) dependent deacetylases that are considered potential targets for metabolic, inflammatory, oncologic, and neurodegenerative disorders. Encoded library technology (ELT) was used to affinity screen a 1.2 million heterocycle enriched library of DNA encoded small molecules, which identified pan-inhibitors of SIRT1/2/3 with nanomolar potency (e.g., 11c: IC50 = 3.6, 2.7, and 4.0 nM for SIRT1, SIRT2, and SIRT3, respectively). Subsequent SAR studies to improve physiochemical properties identified the potent drug like analogues 28 and 31. Crystallographic studies of 11c, 28, and 31 bound in the SIRT3 active site revealed that the common carboxamide binds in the nicotinamide C-pocket and the aliphatic portions of the inhibitors extend through the substrate channel, explaining the observable SAR. These pan SIRT1/2/3 inhibitors, representing a novel chemotype, are significantly more potent than currently available inhibitors, which makes them valuable tools for sirtuin research.

    Organizational Affiliation: 

    Sirtris a GSK Company, Cambridge, Massachusetts, United States. jdisch92@gmail.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrialA285Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1NQ
Query on 1NQ
Download Ideal Coordinates CCD File 
C [auth A]N-{2-[1-(6-carbamoylthieno[3,2-d]pyrimidin-4-yl)piperidin-4-yl]ethyl}-N'-ethylthiophene-2,5-dicarboxamide
C22 H26 N6 O3 S2
IXDTWYVAYLILOL-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1NQ PDBBind:  4JSR IC50: 4 (nM) from 1 assay(s)
Binding MOAD:  4JSR IC50: 4 (nM) from 1 assay(s)
BindingDB:  4JSR IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.32α = 90
b = 119.32β = 90
c = 44.53γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2013-04-24 
    • Deposition Author(s): Dai, H.

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references