1NDV

Crystal Structure of Adenosine Deaminase complexed with FR117016


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A highly potent non-nucleoside adenosine deaminase inhibitor: efficient drug discovery by intentional lead hybridization

Terasaka, T.Kinoshita, T.Kuno, M.Nakanishi, I.

(2004) J.Am.Chem.Soc. 126: 34-35

  • DOI: 10.1021/ja038606l
  • Primary Citation of Related Structures:  1NDW, 1NDY, 1NDZ

  • PubMed Abstract: 
  • We disclose herein the rapid discovery of the first highly potent (Ki = 7.7 nM) non-nucleoside adenosine deaminase (ADA) inhibitor based on the rational hybridization of two structurally distinct leads. Two micromolar inhibitors were discovered by a ...

    We disclose herein the rapid discovery of the first highly potent (Ki = 7.7 nM) non-nucleoside adenosine deaminase (ADA) inhibitor based on the rational hybridization of two structurally distinct leads. Two micromolar inhibitors were discovered by a parallel rational design and random screening program, and individual crystal structures of bovine ADA in complexation with these inhibitors revealed several unknown binding sites and distinct binding modes. Using this information as the starting point, highly effective lead hybridization was achieved in only two structure-based drug design iterations. The conceptual approach illustrated by this example promises to be broadly useful in the search for new chemical entities and can contribute greatly to improve the overall efficiency and speed of drug discovery.


    Organizational Affiliation

    Medicinal Chemistry Research Laboratories, Basic Research Laboratories, and Medicinal Biology Research Laboratories, Fujisawa Pharmaceutical Co., Ltd., 2-1-6, Kashima, Yodogawa-ku, Osaka 532-8514, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine deaminase
A
356Bos taurusGene Names: ADA
EC: 3.5.4.4
Find proteins for P56658 (Bos taurus)
Go to Gene View: ADA
Go to UniProtKB:  P56658
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FR0
Query on FR0

Download SDF File 
Download CCD File 
A
N''-(4-(5-((1H-BENZIMIDAZOL-2-YLAMINO)METHYL)-2-THIENYL)-1,3-THIAZOL-2-YL)GUANIDINE
FR117016
C16 H15 N7 S2
CKJGKHXCUDWFDC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FR0IC50: 700 nM (91) BINDINGDB
FR0Ki: 1200 nM (91) BINDINGDB
FR0Ki: 1200 nM BINDINGMOAD
FR0Ki: 1200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.030α = 90.00
b = 78.030β = 90.00
c = 136.660γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement

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 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance