2pjb: Difference between revisions
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==CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[1-((S)-2-benzyloxycarbonylamino-3-phenyl-propane-1-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEX== | ==CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[1-((S)-2-benzyloxycarbonylamino-3-phenyl-propane-1-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEX== | ||
<StructureSection load='2pjb' size='340' side='right' caption='[[2pjb]], [[Resolution|resolution]] 1.70Å' scene=''> | <StructureSection load='2pjb' size='340' side='right'caption='[[2pjb]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2pjb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PJB OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[2pjb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PJB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PJB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=983:(5S,9R,10R,12S)-12-[3-(AMINOMETHYL)PHENYL]-5-BENZYL-10-HYDROXY-9-ISOPROPYL-3-OXO-1-PHENYL-2-OXA-7-THIA-4,8-DIAZA-10-PHOSPHATRIDECAN-13-OIC+ACID+7,7,10-TRIOXIDE'>983</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=983:(5S,9R,10R,12S)-12-[3-(AMINOMETHYL)PHENYL]-5-BENZYL-10-HYDROXY-9-ISOPROPYL-3-OXO-1-PHENYL-2-OXA-7-THIA-4,8-DIAZA-10-PHOSPHATRIDECAN-13-OIC+ACID+7,7,10-TRIOXIDE'>983</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z5r|1z5r]], [[1zg7|1zg7]], [[1zg8|1zg8]], [[1zg9|1zg9]], [[2piy|2piy]], [[2piz|2piz]], [[2pj0|2pj0]], [[2pj1|2pj1]], [[2pj2|2pj2]], [[2pj3|2pj3]], [[2pj4|2pj4]], [[2pj5|2pj5]], [[2pj6|2pj6]], [[2pj7|2pj7]], [[2pj8|2pj8]], [[2pj9|2pj9]], [[2pja|2pja]], [[2pjc|2pjc]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1z5r|1z5r]], [[1zg7|1zg7]], [[1zg8|1zg8]], [[1zg9|1zg9]], [[2piy|2piy]], [[2piz|2piz]], [[2pj0|2pj0]], [[2pj1|2pj1]], [[2pj2|2pj2]], [[2pj3|2pj3]], [[2pj4|2pj4]], [[2pj5|2pj5]], [[2pj6|2pj6]], [[2pj7|2pj7]], [[2pj8|2pj8]], [[2pj9|2pj9]], [[2pja|2pja]], [[2pjc|2pjc]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carboxypeptidase_B Carboxypeptidase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.2 3.4.17.2] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2pjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pjb OCA], [http://pdbe.org/2pjb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pjb RCSB], [http://www.ebi.ac.uk/pdbsum/2pjb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pjb ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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==See Also== | ==See Also== | ||
*[[Carboxypeptidase|Carboxypeptidase]] | *[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Carboxypeptidase B]] | [[Category: Carboxypeptidase B]] | ||
[[Category: Large Structures]] | |||
[[Category: Sus scrofa]] | [[Category: Sus scrofa]] | ||
[[Category: Adler, M]] | [[Category: Adler, M]] | ||
Revision as of 09:55, 3 June 2020
CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[1-((S)-2-benzyloxycarbonylamino-3-phenyl-propane-1-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEXCRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 2-(3-Aminomethyl-phenyl)-3-{[1-((S)-2-benzyloxycarbonylamino-3-phenyl-propane-1-sulfonylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-propionic acid COMPLEX
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThis 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. 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 Acta Crystallogr D Biol Crystallogr. 2008 Feb;64(Pt 2):149-57. Epub 2008, Jan 16. PMID:18219114[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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