2E1W

Crystal structure of adenosine deaminase complexed with potent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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:  
    2E1W, 1V79, 1V7A

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Adenosine deaminaseA356Bos 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FR6
Query on FR6

Download CCD File 
A
1-{(1R,2S)-2-HYDROXY-1-[2-(1-NAPHTHYL)ETHYL]PROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE
C19 H21 N3 O2
OODDZQQDDOVCFD-SCLBCKFNSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FR6IC50:  16   nM  BindingDB
FR6Ki:  11   nM  BindingDB
FR6Ki:  11   nM  Binding MOAD
FR6Ki :  11   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.41α = 90
b = 78.41β = 90
c = 137.46γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2006-10-30 
  • Released Date: 2006-11-07 
  • Deposition Author(s): Kinoshita, T.
  • This entry supersedes: 1V78

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance