1V79

Crystal structures of adenosine deaminase complexed with potent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 

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:  
    1V79, 1V7A, 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% in rats) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine deaminase A356Bos taurusMutation(s): 0 
Gene Names: ADA
EC: 3.5.4.4
Find proteins for P56658 (Bos taurus)
Explore P56658 
Go to UniProtKB:  P56658
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FR7
Query on FR7

Download Ideal Coordinates CCD File 
A
1-{(1R,2S)-1-[2-(2,3,-DICHLOROPHENYL)ETHYL]-2-HYDROXYPROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE
C15 H17 Cl2 N3 O2
HCJYSIGJDKNVRU-TVQRCGJNSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FR7Ki :  13   nM  PDBBind
FR7IC50:  15   nM  BindingDB
FR7Ki:  13   nM  Binding MOAD
FR7Ki:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.23α = 90
b = 77.23β = 90
c = 135.1γ = 90
Software Package:
Software NamePurpose
crystaldata collection
crystaldata reduction
AMoREphasing
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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