2E1W

Crystal structure of adenosine deaminase complexed with potent inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2E1W/pdb
• Entry: 2E1W supersedes: 1V78

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


• Deposited: 2006-10-30 Released: 2006-11-07 
• Deposition Author(s): Kinoshita, T.

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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 

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

• PubMed: 15139750 
• DOI: https://doi.org/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). 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.

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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: 40.73 kDa 
• Atom Count: 2,935 
• 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
FR6	C [auth A]	1-{(1R,2S)-2-HYDROXY-1-[2-(1-NAPHTHYL)ETHYL]PROPYL}-1H-IMIDAZOLE-4-CARBOXAMIDE C19 H21 N3 O2 OODDZQQDDOVCFD-SCLBCKFNSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FR6	BindingDB:  2E1W	Ki: 11 (nM) from 1 assay(s)
		IC50: 16 (nM) from 1 assay(s)
	PDBBind:  2E1W	Ki: 11 (nM) from 1 assay(s)

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 = 78.41	α = 90
b = 78.41	β = 90
c = 137.46	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNX	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations