1WXZ

Crystal structure of adenosine deaminase ligated with a potent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1WXZ/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2005-02-02 Released: 2005-08-16 
• Deposition Author(s): Kinoshita, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

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

• PubMed: 16033254 
• 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.83 kDa 
• Atom Count: 2,958 
• Modelled Residue Count: 349 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosine deaminase	A	356	Bos taurus	Mutation(s): 0  EC: 3.5.4.4
UniProt
Find proteins for P56658 (Bos taurus) Explore P56658  Go to UniProtKB:  P56658

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRL	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	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.223 (Depositor) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.8	α = 90
b = 77.8	β = 90
c = 137.4	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-16 
Deposition Author(s): Kinoshita, T.

Revision History  

• 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