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


Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/s41589-018-0150-0
  • Primary Citation of Related Structures:  
    5Y2F

  • 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 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

    Key Laboratory of Cell Differentiation and Apoptosis, Ministry of Education, Department of Pathophysiology, Ruijin Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-6316Homo sapiensMutation(s): 0 
Gene Names: SIRT6SIR2L6
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N6T7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
9-mer peptide QTARKSTGGB [auth C]9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8L9
Query on 8L9

Download Ideal Coordinates CCD File 
D [auth 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
AR6
Query on AR6

Download Ideal Coordinates CCD File 
C [auth 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
HDR
Query on HDR

Download Ideal Coordinates CCD File 
R [auth C]HEXADECANE-1-SULFINIC ACID
C16 H34 O2 S
HBTBNXFVJYRYGI-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
Q [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth A]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
S [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8L9 BindingDB:  5Y2F EC50: min: 5700, max: 1.00e+4 (nM) from 2 assay(s)
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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