4I5I

Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog

Structural Biology Knowledgebase: 4I5I SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.167

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I5I

Classification: HYDROLASE

Total Structure Weight: 67024.99

Macromolecule Entities
Molecule Chains Length Organism Details
NAD-dependent protein deacetylase sirtuin-1 A, B 287 Homo sapiens EC#: 3.5.1 IUBMB
Fragment: Deacetylase sirtuin-type catalytic domain residues 241-516
Gene Name(s): SIRT1 Gene View SIR2L1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
4I5
Query on 4I5

A, B (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole- 6-carboxamide
C14 H15 Cl N2 O
ABIVOOWWGYJNLV-JTQLQIEISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4I5 IC50: 63 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.195
  • R-Value Work: 0.167
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 106.51 α = 90.00
b = 106.51 β = 90.00
c = 80.66 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-28
  • Released Date: 2013-01-23
  • Deposition author(s): Zhao, X., Allison, D., Condon, B., Zhang, F., Gheyi, T., Zhang, A., Ashok, S., Russell, M., Macewan, I., Qian, Y., Jamison, J.A., Luz, J.G.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --
  • 2013-08-28
    Type: Citation | Details: Citation update