3WAB

Carboxypeptidase B in complex with DD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: Selenium coordinates to zinc in enzyme

Yoshimoto, N.Itoh, T.Inaba, Y.Ishii, H.Yamamoto, K.

(2013) J Med Chem 

  • DOI: 10.1021/jm400816v
  • Primary Citation of Related Structures:  
    3WAB, 3WC7, 3WC5, 3WC6

  • PubMed Abstract: 
  • Activated thrombin-activatable fibrinolysis inhibitor (TAFIa) is a zinc-containing carboxypeptidase and significantly inhibits fibrinolysis. TAFIa inhibitors are thus expected to act as profibrinolytic agents. We recently reported the design and synt ...

    Activated thrombin-activatable fibrinolysis inhibitor (TAFIa) is a zinc-containing carboxypeptidase and significantly inhibits fibrinolysis. TAFIa inhibitors are thus expected to act as profibrinolytic agents. We recently reported the design and synthesis of selenium-containing inhibitors of TAFIa and their inhibitory activity. Here we report the crystal structures of potent selenium-, sulfur-, and phosphinic acid-containing inhibitors bound to porcine pancreatic carboxypeptidase B (ppCPB). ppCPB is a TAFIa homologue and is surrogate TAFIa for crystallographic analysis. Crystal structures of ppCPB complexed with selenium compound 1a, its sulfur analogue 2, and phosphinic acid derivative EF6265 were determined at 1.70, 2.15, and 1.90 Å resolution, respectively. Each inhibitor binds to the active site of ppCPB in a similar manner to that observed for previously reported inhibitors. Thus, in complexes, selenium, sulfur, and phosphinic acid oxygen coordinate to zinc in ppCPB. This is the first observation and report of selenium coordinating to zinc in CPB.


    Organizational Affiliation

    High Technology Research Center, ‡Laboratory of Drug Design and Medicinal Chemistry and §Laboratory of Molecular and Cellular Pathophysiology, Showa Pharmaceutical University , 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carboxypeptidase BA306Sus scrofaMutation(s): 0 
Gene Names: CPB1CPB
EC: 3.4.17.2
Find proteins for P09955 (Sus scrofa)
Explore P09955 
Go to UniProtKB:  P09955
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DDW
Query on DDW

Download CCD File 
A
(2R)-7-amino-2-(sulfanylmethyl)heptanoic acid
C8 H17 N O2 S
OWVFNXQLXNWAHW-ZETCQYMHSA-N
 Ligand Interaction
CAC
Query on CAC

Download CCD File 
A
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DDWIC50:  3.5999999046325684   nM  BindingDB
DDWIC50 :  34   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.314α = 90
b = 79.314β = 90
c = 100.342γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
RAPID-AUTOdata collection
RAPID-AUTOdata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release