3FX6

X-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization of alpha-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A

Wang, S.F.Tian, G.R.Zhang, W.Z.Jin, J.Y.

(2009) Bioorg Med Chem Lett 19: 5009-5011

  • DOI: 10.1016/j.bmcl.2009.07.060
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Zinc-binding groups (ZBGs) are exhaustively applied in the development of the new inhibitors against a wide variety of physiologically and pathologically important zinc proteases. Here the alpha-nitro ketone was presented as a new ZBG, which is a tra ...

    Zinc-binding groups (ZBGs) are exhaustively applied in the development of the new inhibitors against a wide variety of physiologically and pathologically important zinc proteases. Here the alpha-nitro ketone was presented as a new ZBG, which is a transition-state analog featured by the unique bifurcated hydrogen bonds at the active site of carboxypeptidase A based on the structural analysis. Introduction of a nitro group at the alpha-position of the ketone could provide more non-covalent interactions without loss of the abilities to form a tetrahedral transition-state analog.


    Organizational Affiliation

    Key Laboratory of Biological Resources and Functional Molecules of the Changbai Mountains, Ministry of Education, Yanbian University, Yanji, Jilin, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A1
A, C, E
307Bos taurusMutation(s): 0 
Gene Names: CPA1CPA
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to UniProtKB:  P00730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BPX
Query on BPX

Download CCD File 
A, C, E
(2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid
C12 H15 N O6
CGGNZMVODZPHHK-SNVBAGLBSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BPXKi:  160   nM  Binding MOAD
BPXKi :  160   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.356α = 90
b = 59.752β = 104.04
c = 99.514γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description