5Y2F

Human SIRT6 in complex with allosteric activator MDL-801


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of a cellularly active SIRT6 allosteric activator.

Huang, Z.Zhao, J.Deng, W.Chen, Y.Shang, J.Song, K.Zhang, L.Wang, C.Lu, S.Yang, X.He, B.Min, J.Hu, H.Tan, M.Xu, J.Zhang, Q.Zhong, J.Sun, X.Mao, Z.Lin, H.Xiao, M.Chin, Y.E.Jiang, H.Xu, Y.Chen, G.Zhang, J.

(2018) Nat Chem Biol 14: 1118-1126

  • DOI: 10.1038/s41589-018-0150-0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • SIRT6, a member of the SIRT deacetylase family, is responsible for deacetylation of histone H3 N ε -acetyl-lysines 9 (H3K9ac) and 56 (H3K56ac). As a tumor suppressor, SIRT6 has frequently been found to have low expression in various cancer ...

    SIRT6, a member of the SIRT deacetylase family, is responsible for deacetylation of histone H3 N ε -acetyl-lysines 9 (H3K9ac) and 56 (H3K56ac). As a tumor suppressor, SIRT6 has frequently been found to have low expression in various cancers. Here, we report the identification of MDL-800, a selective SIRT6 activator. MDL-800 increased the deacetylase activity of SIRT6 by up to 22-fold via binding to an allosteric site; this interaction led to a global decrease in H3K9ac and H3K56ac levels in human hepatocellular carcinoma (HCC) cells. Consequently, MDL-800 inhibited the proliferation of HCC cells via SIRT6-driven cell-cycle arrest and was effective in a tumor xenograft model. Together, these data demonstrate that pharmacological activation of SIRT6 is a potential therapeutic approach for the treatment of HCC. MDL-800 is a first-in-class small-molecule cellular SIRT6 activator that can be used to physiologically and pathologically investigate the roles of SIRT6 deacetylation.


    Organizational Affiliation

    Medicinal Bioinformatics Center, Shanghai JiaoTong University School of Medicine, Shanghai, China. jian.zhang@sjtu.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-6
A
316Homo sapiensMutation(s): 0 
Gene Names: SIRT6SIR2L6
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q8N6T7 (Homo sapiens)
Go to UniProtKB:  Q8N6T7
NIH Common Fund Data Resources
PHAROS  Q8N6T7
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
9-mer peptide QTARKSTGG
C
9Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8L9
Query on 8L9

Download CCD File 
A
5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid
C20 H14 Br Cl2 F N2 O6 S2
MJYYUGUIBHEWRX-UHFFFAOYSA-N
 Ligand Interaction
AR6
Query on AR6

Download CCD File 
A
[(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
 Ligand Interaction
HDR
Query on HDR

Download CCD File 
C
HEXADECANE-1-SULFINIC ACID
C16 H34 O2 S
HBTBNXFVJYRYGI-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.422α = 90
b = 162.422β = 90
c = 162.422γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data processing
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 1.2: 2018-11-28
    Changes: Data collection, Database references