4JT9

Crystal Structure of human SIRT3 with ELT inhibitor 3 [14-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide]

Structural Biology Knowledgebase: 4JT9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JT9

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 32268.64

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacetylase sirtuin-3, mitochondrial A 285 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: UNP residues 118-399
Gene Name(s): SIRT3 Gene View SIR2L3

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
1NS
Query on 1NS

A 4-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin- 1-yl)thieno[3,2-d]pyrimidine-6-carboxamide
C15 H21 N5 O3 S2
BKOWIHMCGFRARN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1NS N/A in BindingDB
IC50: 7.2 nM  BindingMOAD
IC50: 7.2 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.197
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 120.46 α = 90.00
b = 120.46 β = 90.00
c = 44.47 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-03-22
  • Released Date: 2013-04-24
  • Deposition author(s): Dai, H.

Revision History

  • 2013-07-03
    Type: Citation | Details: Citation update