1V79

Crystal structures of adenosine deaminase complexed with potent inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 

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:  

  • 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 taurusMutation(s): 0 
Gene 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
FR7
Query on FR7
Download SDF File 
Download CCD File 
A
1-{(1R,2S)-1-[2-(2,3,-DICHLOROPHENYL)ETHYL]-2-HYDROXYPROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE
FR239087
C15 H17 Cl2 N3 O2
HCJYSIGJDKNVRU-TVQRCGJNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FR7IC50: 15 nM (91) BINDINGDB
FR7Ki: 13 nM (91) BINDINGDB
FR7Ki: 13 nM BINDINGMOAD
FR7Ki: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.252 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.230α = 90.00
b = 77.230β = 90.00
c = 135.100γ = 90.00
Software Package:
Software NamePurpose
crystaldata collection
CrystalCleardata scaling
AMoREphasing
crystaldata reduction
CNXrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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