1S5Z

NDP kinase in complex with adenosine phosphonoacetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Adenosine phosphonoacetic acid is slowly metabolized by NDP kinase.

Chen, Y.Morera, S.Pasti, C.Angusti, A.Solaroli, N.Veron, M.Janin, J.Manfredini, S.Deville-Bonne, D.

(2005) Med Chem 1: 529-536

  • DOI: 10.2174/157340605774598162
  • Primary Citation of Related Structures:  
    1S5Z

  • PubMed Abstract: 
  • NDP kinase catalyzes the last step in the phosphorylation of nucleotides. It is also involved in the activation by cellular kinases of nucleoside analogs used in antiviral therapies. Adenosine phosphonoacetic acid, a close analog of ADP already proposed as an inhibitor of ribonucleotide reductase, was found to be a poor substrate for human NDP kinase, as well as a weak inhibitor with an equilibrium dissociation constant of 0 ...

    NDP kinase catalyzes the last step in the phosphorylation of nucleotides. It is also involved in the activation by cellular kinases of nucleoside analogs used in antiviral therapies. Adenosine phosphonoacetic acid, a close analog of ADP already proposed as an inhibitor of ribonucleotide reductase, was found to be a poor substrate for human NDP kinase, as well as a weak inhibitor with an equilibrium dissociation constant of 0.6 mM to be compared to 0.025 mM for ADP. The X-ray structure of a complex of adenosine phosphonoacetic acid and the NDP kinase from Dictyostelium was determined to 2.0 A resolution showing that the analog adopts a binding mode similar to ADP, but that no magnesium ion is present at the active site. As ACP may also interfere with other cellular kinases, its potential as a drug targeting NDP kinase or ribonucleotide reductase is likely to be limited due to strong side effects. The design of new molecules with a narrower specificity and a stronger affinity will benefit from the detailed knowledge of the complex ACP-NDP kinase.


    Organizational Affiliation

    Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS UPR 9063, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase, cytosolic
A, B, C, D, E, F
A, B, C, D, E, F
155Dictyostelium discoideumMutation(s): 0 
Gene Names: NDKCndkBgip17DD_02290DD_02289ndkC-1DDB_G0273069ndkC-2DDB_G0273805
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SON
Query on SON

Download Ideal Coordinates CCD File 
G [auth A]ADENOSINE PHOSPHONOACETIC ACID
C12 H16 N5 O8 P
KJNLSEOJEFDELT-JJNLEZRASA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SON PDBBind:  1S5Z Kd: 6.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.38α = 90
b = 104.594β = 118.28
c = 69.569γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance