7T1D | pdb_00007t1d

Human SIRT2 in complex with small molecule 359


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.213 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.174 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7T1D

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An allosteric inhibitor of sirtuin 2 deacetylase activity exhibits broad-spectrum antiviral activity.

Roche, K.L.Remiszewski, S.Todd, M.J.Kulp 3rd, J.L.Tang, L.Welsh, A.V.Barry, A.P.De, C.Reiley, W.W.Wahl, A.Garcia, J.V.Luftig, M.A.Shenk, T.Tonra, J.R.Murphy, E.A.Chiang, L.W.

(2023) J Clin Invest 133

  • DOI: https://doi.org/10.1172/JCI158978
  • Primary Citation Related Structures: 
    7T1D

  • PubMed Abstract: 

    Most drugs used to treat viral disease target a virus-coded product. They inhibit a single virus or virus family, and the pathogen can readily evolve resistance. Host-targeted antivirals can overcome these limitations. The broad-spectrum activity achieved by host targeting can be especially useful in combating emerging viruses and for treatment of diseases caused by multiple viral pathogens, such as opportunistic agents in immunosuppressed patients. We have developed a family of compounds that modulate sirtuin 2, an NAD+-dependent deacylase, and now report the properties of a member of that family, FLS-359. Biochemical and x-ray structural studies show that the drug binds to sirtuin 2 and allosterically inhibits its deacetylase activity. FLS-359 inhibits the growth of RNA and DNA viruses, including members of the coronavirus, orthomyxovirus, flavivirus, hepadnavirus, and herpesvirus families. FLS-359 acts at multiple levels to antagonize cytomegalovirus replication in fibroblasts, causing modest reductions in viral RNAs and DNA, together with a much greater reduction in infectious progeny, and it exhibits antiviral activity in humanized mouse models of infection. Our results highlight the potential of sirtuin 2 inhibitors as broad-spectrum antivirals and set the stage for further understanding of how host epigenetic mechanisms impact the growth and spread of viral pathogens.


  • Organizational Affiliation
    • Evrys Bio LLC, Pennsylvania Biotechnology Center, Doylestown, Pennsylvania, USA.

Macromolecule Content 

  • Total Structure Weight: 70.22 kDa 
  • Atom Count: 5,713 
  • Modeled Residue Count: 590 
  • Deposited Residue Count: 602 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-2
A, B
301Homo sapiensMutation(s): 0 
Gene Names: SIRT2
EC: 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens)
Explore Q8IXJ6 
Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6
GTEx:  ENSG00000068903 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXJ6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E7K
(Subject of Investigation/LOI)

Query on E7K



Download:Ideal Coordinates CCD File
I [auth A],
S [auth B]
7-(2,4-dimethyl-1H-imidazol-1-yl)-2-(5-{[4-(1H-pyrazol-1-yl)phenyl]methyl}-1,3-thiazol-2-yl)-1,2,3,4-tetrahydroisoquinoline
C27 H26 N6 S
JRPPFSVORXBCPF-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
H [auth A],
R [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
M [auth B]
N [auth B]
O [auth B]
F [auth A],
G [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.213 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.174 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.775α = 90
b = 55.98β = 94.462
c = 139.576γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR44AI122488

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-04-03
    Changes: Refinement description