2PJ5

CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B [((R)-1-Benzyloxycarbonylamino-hexyl)-hydroxy-phosphinoyloxy]-(3-guanidino-phenyl)-acetic acid COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of potent selective peptide mimetics bound to carboxypeptidase B.

Adler, M.Buckman, B.Bryant, J.Chang, Z.Chu, K.Emayan, K.Hrvatin, P.Islam, I.Morser, J.Sukovich, D.West, C.Yuan, S.Whitlow, M.

(2008) Acta Crystallogr.,Sect.D 64: 149-157

  • DOI: 10.1107/S0907444907057228
  • Primary Citation of Related Structures:  2PIY, 2PIZ, 2PJ0, 2PJ1, 2PJ2, 2PJ3, 2PJ4, 2PJ6, 2PJ7, 2PJ8, 2PJ9, 2PJA, 2PJB, 2PJC

  • PubMed Abstract: 
  • This article reports the crystal structures of inhibitors of the functional form of thrombin-activatable fibrinolysis inhibitor (TAFIa). In vivo experiments indicate that selective inhibitors of TAFIa would be useful in the treatment of heart attacks ...

    This article reports the crystal structures of inhibitors of the functional form of thrombin-activatable fibrinolysis inhibitor (TAFIa). In vivo experiments indicate that selective inhibitors of TAFIa would be useful in the treatment of heart attacks. Since TAFIa rapidly degrades in solution, the homologous protein porcine pancreatic carboxypeptidase B (pp-CpB) was used in these crystallography studies. Both TAFIa and pp-CpB are zinc-based exopeptidases that are specific for basic residues. The final development candidate, BX 528, is a potent inhibitor of TAFIa (2 nM) and has almost no measurable effect on the major selectivity target, carboxypeptidase N. BX 528 was designed to mimic the tripeptide Phe-Val-Lys. A sulfonamide replaces the Phe-Val amide bond and a phosphinate connects the Val and Lys groups. The phosphinate also chelates the active-site zinc. The electrostatic interactions with the protein mimic those of the natural substrate. The primary amine in BX 528 forms a salt bridge to Asp255 at the base of the S1' pocket. The carboxylic acid interacts with Arg145 and the sulfonamide is hydrogen bonded to Arg71. Isopropyl and phenyl groups replace the side chains of Val and Phe, respectively. A series of structures are presented here that illustrate the evolution of BX 528 from thiol-based inhibitors that mimic a free C-terminal arginine. The first step in development was the replacement of the thiol with a phosphinate. This caused a precipitous drop in binding affinity. Potency was reclaimed by extending the inhibitors into the downstream binding sites for the natural substrate.


    Related Citations: 
    • Crystal Structures of Potent Thiol-Based Inhibitors Bound to Carboxypeptidase B.
      Adler, M.,Bryant, J.,Buckman, B.,Islam, I.,Larsen, B.,Finster, S.,Kent, L.,May, K.,Mohan, R.,Yuan, S.,Whitlow, M.
      (2005) Biochemistry 44: 9339
    • 3-Mercaptopropionic acids as efficacious inhibitors of activated thrombin activatable fibrinolysis inhibitor (TAFIa).
      Islam, I.,Bryant, J.,May, K.,Mohan, R.,Yuan, S.,Kent, L.,Morser, J.,Zhao, L.,Vergona, R.,White, K.,Adler, M.,Whitlow, M.,Buckman, B.O.
      (2007) Bioorg.Med.Chem.Lett. 17: 1349


    Organizational Affiliation

    Bayer HealthCare Pharmaceuticals, 2600 Hilltop Drive, PO Box 4099, Richmond, California 94804-0099, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase B
A, B, C
306Sus scrofaGene Names: CPB1 (CPB)
EC: 3.4.17.2
Find proteins for P09955 (Sus scrofa)
Go to Gene View: CPB1
Go to UniProtKB:  P09955
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
11B
Query on 11B

Download SDF File 
Download CCD File 
A, B, C
(5R,6S,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-6-HYDROXY-3-OXO-5-PENTYL-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID 6-OXIDE
C23 H31 N4 O7 P
XFGOBDZHGXXQBF-UXHICEINSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
11BIC50: 15 nM BINDINGMOAD
11BIC50: 15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.805α = 90.00
b = 96.145β = 90.00
c = 135.875γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-04-15 
  • Released Date: 2008-01-22 
  • Deposition Author(s): Adler, M., Whitlow, M.

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance