2PJ8

CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[(R)-1-(biphenyl-4-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEX

PDB DOI: 10.2210/pdb2PJ8/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.200
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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 D Biol Crystallogr 64: 149-157

PubMed: 18219114 Search on PubMed
DOI: 10.1107/S0907444907057228
Primary Citation of Related Structures:
2PIY, 2PIZ, 2PJ0, 2PJ1, 2PJ2, 2PJ3, 2PJ4, 2PJ5, 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. 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:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase B	A, B, C	306	Sus scrofa	Mutation(s): 0 Gene Names: CPB1, CPB EC: 3.4.17.2
UniProt
Find proteins for P09955 (Sus scrofa) Explore P09955 Go to UniProtKB: P09955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09955
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
17A Query on 17A Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	(2S)-2-[3-(AMINOMETHYL)PHENYL]-3-[(R)-{(1R)-1-[(BIPHENYL-4-YLSULFONYL)AMINO]-2-METHYLPROPYL}(HYDROXY)PHOSPHORYL]PROPANOIC ACID C₂₆ H₃₁ N₂ O₆ P S KEOUUUFVAPIYKJ-LOSJGSFVSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction