5ZEQ

Carboxypeptidase B in complex with DD28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the selective inhibition of activated thrombin-activatable fibrinolysis inhibitor (TAFIa) by a selenium-containing inhibitor with chloro-aminopyridine as a basic group

Itoh, T.Yoshimoto, N.Hirano, Y.Yamamoto, K.

(2018) Bioorg Med Chem Lett 28: 2256-2260

  • DOI: 10.1016/j.bmcl.2018.05.042
  • Primary Citation of Related Structures:  
    5ZEQ

  • PubMed Abstract: 
  • Activated thrombin-activatable fibrinolysis inhibitor (TAFIa) is a target molecule for treating thromboembolic disorders. We previously reported that design and synthesis of compound 1 containing a selenol group and chloloaminopyridine. Compound 1 showed high inhibitory activity towards TAFIa, with a high degree of selectivity for TAFIa over carboxypeptidase N (CPN) ...

    Activated thrombin-activatable fibrinolysis inhibitor (TAFIa) is a target molecule for treating thromboembolic disorders. We previously reported that design and synthesis of compound 1 containing a selenol group and chloloaminopyridine. Compound 1 showed high inhibitory activity towards TAFIa, with a high degree of selectivity for TAFIa over carboxypeptidase N (CPN). Here we report investigation of this selectivity. To obtain co-crystal of 1/pp-CPB (a surrogate of TAFIa), we synthesized protected compound 5 as a stabilized precursor of 1. The X-ray crystal structure and docking study indicated that the Cl substituent is accommodated in the pp-CPB specific pocket whereas CPN has no identical pocket. This is important information for the design of drugs targeting TAFIa with high selectivity.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: yamamoto@ac.shoyaku.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carboxypeptidase BA304Sus scrofaMutation(s): 0 
Gene Names: CPB1CPB
EC: 3.4.17.2
UniProt
Find proteins for P09955 (Sus scrofa)
Explore P09955 
Go to UniProtKB:  P09955
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.155 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.86α = 90
b = 78.86β = 90
c = 100.04γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references