2I6A

Human Adenosine Kinase in Complex With 5'-Deoxy-5-Iodotubercidin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of human adenosine kinase inhibitor complexes reveal two distinct binding modes.

Muchmore, S.W.Smith, R.A.Stewart, A.O.Cowart, M.D.Gomtsyan, A.Matulenko, M.A.Yu, H.Severin, J.M.Bhagwat, S.S.Lee, C.H.Kowaluk, E.A.Jarvis, M.F.Jakob, C.L.

(2006) J.Med.Chem. 49: 6726-6731

  • DOI: 10.1021/jm060189a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adenosine kinase (AK) is an enzyme responsible for converting endogenous adenosine (ADO) to adenosine monophosphate (AMP) in an adenosine triphosphate- (ATP-) dependent manner. The structure of AK consists of two domains, the first a large alpha/beta ...

    Adenosine kinase (AK) is an enzyme responsible for converting endogenous adenosine (ADO) to adenosine monophosphate (AMP) in an adenosine triphosphate- (ATP-) dependent manner. The structure of AK consists of two domains, the first a large alpha/beta Rossmann-like nucleotide binding domain that forms the ATP binding site, and a smaller mixed alpha/beta domain, which, in combination with the larger domain, forms the ADO binding site and the site of phosphoryl transfer. AK inhibitors have been under investigation as antinociceptive, antiinflammatory, and anticonvulsant as well as antiinfective agents. In this work, we report the structures of AK in complex with two classes of inhibitors: the first, ADO-like, and the second, a novel alkynylpyrimidine series. The two classes of structures, which contain structurally similar substituents, reveal distinct binding modes in which the AK structure accommodates the inhibitor classes by a 30 degrees rotation of the small domain relative to the large domain. This change in binding mode stabilizes an open and a closed intermediate structural state and provide structural insight into the transition required for catalysis. This results in a significant rearrangement of both the protein active site and the orientation of the alkynylpyrimidine ligand when compared to the observed orientation of nucleosidic inhibitors or substrates.


    Organizational Affiliation

    Structural Biology, R46Y, and Neuroscience Research, R4PM, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064, USA. steve.w.muchmore@abbott.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenosine kinase
A, B, C, D
345Homo sapiensMutation(s): 0 
Gene Names: ADK
EC: 2.7.1.20
Find proteins for P55263 (Homo sapiens)
Go to Gene View: ADK
Go to UniProtKB:  P55263
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5I5
Query on 5I5

Download SDF File 
Download CCD File 
A, B, C, D
7-(5-DEOXY-BETA-D-RIBOFURANOSYL)-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
5'-DEOXY-5-IODOTUBERCIDIN; (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(METHYL)TETRAHYDROFURAN-3,4-DIOL
C11 H13 I N4 O3
NTXUAWGNGBSCRS-TZQXKBMNSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5I5IC50: 0.9 - 22.8 nM (90) BINDINGDB
5I5IC50: 0.9 nM BINDINGMOAD
5I5IC50: 0.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.850α = 97.76
b = 66.930β = 103.70
c = 87.140γ = 89.95
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
DMphasing
DMmodel building
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-08-28 
  • Released Date: 2007-01-02 
  • Deposition Author(s): Muchmore, S.W.

Revision History 

  • Version 1.0: 2007-01-02
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description