1V7A

Crystal structures of adenosine deaminase complexed with potent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design and synthesis of non-nucleoside, potent, and orally bioavailable adenosine deaminase inhibitors

Terasaka, T.Okumura, H.Tsuji, K.Kato, T.Nakanishi, I.Kinoshita, T.Kato, Y.Kuno, M.Seki, N.Naoe, Y.Inoue, T.Tanaka, K.Nakamura, K.

(2004) J.Med.Chem. 47: 2728-2731

  • DOI: 10.1021/jm0499559
  • Primary Citation of Related Structures:  1V78, 1V79, 2E1W

  • PubMed Abstract: 
  • We disclose optimization efforts based on the novel non-nucleoside adenosine deaminase (ADA) inhibitor, 4 (K(i) = 680 nM). Structure-based drug design utilizing the crystal structure of the 4/ADA complex led to discovery of 5 (K(i) = 11 nM, BA = 30% ...

    We disclose optimization efforts based on the novel non-nucleoside adenosine deaminase (ADA) inhibitor, 4 (K(i) = 680 nM). Structure-based drug design utilizing the crystal structure of the 4/ADA complex led to discovery of 5 (K(i) = 11 nM, BA = 30% in rats). Furthermore, from metabolic considerations, we discovered two inhibitors with improved oral bioavailability [6 (K(i) = 13 nM, BA = 44%) and 7 (K(i) = 9.8 nM, BA = 42%)]. 6 demonstrated in vivo efficacy in models of inflammation and lymphoma.


    Organizational Affiliation

    Medicinal Chemistry Research Laboratories, Fujisawa Pharmaceutical Co., Ltd., 2-1-6, Kashima, Yodogawa-ku, Osaka 532-8514, Japan. tadashi_terasaka@po.fujisawa.co.jp




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
FRC
Query on FRC

Download SDF File 
Download CCD File 
A
1-{(1R,2S)-2-HYDROXY-1-[2-(2-NAPHTHYLOXY)ETHYL]PROPYL}-1H-IMIDAZONE-4-CARBOXAMIDE
FR247581
C19 H21 N3 O3
UYAJDVNLQJVRHD-SCLBCKFNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRCKi: 9.8 nM (91) BINDINGDB
FRCKi: 9.8 nM BINDINGMOAD
FRCKi: 9.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.244 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.520α = 90.00
b = 77.520β = 90.00
c = 136.200γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
crystaldata reduction
AMoREphasing
CrystalCleardata scaling
CNXrefinement
crystaldata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-12-14 
  • Released Date: 2004-12-21 
  • Deposition Author(s): Kinoshita, T.

Revision History 

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance