5MFP | pdb_00005mfp

Human Sirt6 in complex with activator UBCS58

• PDB DOI: https://doi.org/10.2210/pdb5MFP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-18 Released: 2016-12-28 
• Deposition Author(s): Steegborn, C., You, W., Kambach, C.
• Funding Organization(s): Oberfrankenstiftung

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.157 (Depositor) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of Sirtuin 6 Activation by Synthetic Small Molecules.

You, W., Rotili, D., Li, T.M., Kambach, C., Meleshin, M., Schutkowski, M., Chua, K.F., Mai, A., Steegborn, C.

(2017) Angew Chem Int Ed Engl 56: 1007-1011

• PubMed: 27990725 
• DOI: https://doi.org/10.1002/anie.201610082
• Primary Citation Related Structures: 
  5MF6, 5MFP, 5MFZ, 5MGN


• PubMed Abstract: 
  

  Sirtuins are protein deacylases regulating metabolism and stress responses, and are implicated in aging-related diseases. Small molecule activators for the human sirtuins Sirt1-7 are sought as chemical tools and potential therapeutics, such as for cancer. Activators are available for Sirt1 and exploit its unique N-terminus, whereas drug-like activators for Sirt2-7 are lacking. We synthesized and screened pyrrolo[1,2-a]quinoxaline derivatives, yielding the first synthetic Sirt6 activators. Biochemical assays show direct, substrate-independent compound binding to the Sirt6 catalytic core and potent activation of Sirt6-dependent deacetylation of peptide substrates and complete nucleosomes. Crystal structures of Sirt6/activator complexes reveal that the compounds bind to a Sirt6-specific acyl channel pocket and identify key interactions. Our results establish potent Sirt6 activation with small molecules and provide a structural basis for further development of Sirt6 activators as tools and therapeutics.

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Organizational Affiliation: 
• Universität Bayreuth, Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle, Universitätsstr. 30, 95447, Bayreuth, Germany.
Sapienza University Roma, Department of Drug Chemistry and Technologies and Pasteur Institute of the Cenci-Bolognetti Foundation, P. le A. Moro 5, 00185, Rome, Italy.
Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive Grant Bldg., Rm. S-025, Stanford, CA, 94305, USA.
Geriatric Research, Education, and Clinical Center, Department of Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
Abteilung Enzymology, Institut für Biochemie und Biotechnologie, Martin-Luther-Universität, Kurt-Mothes-Str. 3, 06110, Halle (Saale), Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.46 kDa 
• Atom Count: 4,719 
• Modeled Residue Count: 557 
• Deposited Residue Count: 604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-6	A, B	302	Homo sapiens	Mutation(s): 0  Gene Names: SIRT6, SIR2L6 EC: 3.5.1 (PDB Primary Data), 2.4.2 (UniProt), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T7 (Homo sapiens) Explore Q8N6T7  Go to UniProtKB:  Q8N6T7
PHAROS:  Q8N6T7 GTEx:  ENSG00000077463

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	C [auth A], N [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
7M5	M [auth A], W [auth B]	4-pyridin-3-ylpyrrolo[1,2-a]quinoxaline C16 H11 N3 YYLFSLFSCWVKLI-UHFFFAOYSA-N
PG4	L [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	T [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.157 (Depositor) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.38	α = 90
b = 91.38	β = 90
c = 144.148	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-28 
Deposition Author(s): Steegborn, C., You, W., Kambach, C.

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Funding Organization	Location	Grant Number
Oberfrankenstiftung	Germany	--

Revision History  

• Version 1.0: 2016-12-28
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary