1NDY

Crystal Structure of Adenosine Deaminase Complexed with FR230513

Structural Biology Knowledgebase: 1NDY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1NDY

Classification: hydrolase

Total Structure Weight: 40716.81

Macromolecule Entities
Molecule Chains Length Organism Details
Adenosine Deaminase A 356 Bos taurus EC#: 3.5.4.4 IUBMB
Mutation: N8D, R32K, K33R, S57T, E60D, E77D, V79I, K199Q, A246T, V261I, P279A, V281I, N313K, E314D, G352R
Gene Name(s): ADA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FR3
Query on FR3

A 1-((1R)-1-(HYDROXYMETHYL)-3-(1-NAPHTHYL)PROPYL)- 1H-IMIDAZOLE-4-CARBOXAMIDE
FR230513 (Synonym)
C18 H19 N3 O2
URGFTPMACWKJKU-OAHLLOKOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FR3 IC50: 570 nM (91) BindingDB
Ki: 680 nM (91) BindingDB

Ki: 680 nM  BindingMOAD
Ki: 680 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.203
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 77.92 α = 90.00
b = 77.92 β = 90.00
c = 136.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-12-09
  • Released Date: 2003-12-09
  • Deposition author(s): Kinoshita, T.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4