1WXZ

Crystal structure of adenosine deaminase ligated with a potent inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Rational design of non-nucleoside, potent, and orally bioavailable adenosine deaminase inhibitors: predicting enzyme conformational change and metabolism

Terasaka, T., Tsuji, K., Kato, T., Nakanishi, I., Kinoshita, T., Kato, Y., Kuno, M., Inoue, T., Tanaka, K., Nakamura, K.

(2005) J Med Chem 48: 4750-4753

  • DOI: https://doi.org/10.1021/jm050413g
  • Primary Citation of Related Structures:  
    1WXZ

  • PubMed Abstract: 

    From metabolic considerations and prediction of an inhibitor-induced conformational change, novel adenosine deaminase (ADA) inhibitors with improved activities and oral bioavailability have been developed on the basis of our originally designed non-nucleoside ADA inhibitors. They demonstrated in vivo efficacy in models of inflammation and lymphoma. Furthermore, X-ray crystal structure analysis has revealed a novel induced fit to ADA.

    • Organizational Affiliation: 

    Medicinal Chemistry Research Laboratories, Fujisawa Pharmaceutical Co., Ltd., 2-1-6, Kashima, Yodogawa-ku, Osaka 532-8514, Japan. tadashi.terasaka@jp.astellas.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine deaminase356Bos taurusMutation(s): 0 
EC: 3.5.4.4
UniProt
Find proteins for P56658 (Bos taurus)
Explore P56658 
Go to UniProtKB:  P56658
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56658
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FRL
Query on FRL
Download Ideal Coordinates CCD File 
C [auth A]1-((1R,2S)-1-{2-[2-(4-CHLOROPHENYL)-1,3-BENZOXAZOL-7-YL]ETHYL}-2-HYDROXYPROPYL)-1H-IMIDAZOLE-4-CARBOXAMIDE
C22 H21 Cl N4 O3
SMFRBBHLVBWHGB-DJJJIMSYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FRL PDBBind:  1WXZ IC50: 8.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.8α = 90
b = 77.8β = 90
c = 137.4γ = 90
Software Package:
Software NamePurpose
CNXrefinement
CrystalCleardata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations