1bb0

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[[Image:1bb0.gif|left|200px]]<br />
 
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<applet load="1bb0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bb0, resolution 2.1&Aring;" />
 
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'''THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES'''<br />
 
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==Overview==
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==THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES==
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The crystal structures of three highly potent and selective low-molecular, weight rigid peptidyl aldehyde inhibitors complexed with thrombin have, been determined and refined to R values 0.152-0. 170 at 1.8-2.1 A, resolution. Since the selectivity of two of the inhibitors was &gt;1600 with, respect to trypsin, the structures of trypsin-inhibited complexes of these, inhibitors were also determined (R = 0.142-0.157 at 1.9-2.1 A resolution)., The selectivity appears to reside in the inability of a benzenesulfonamide, group to bind at the equivalent of the D-enantiomorphic S3 site of, thrombin, which may be related to the lack of a 60-insertion loop in, trypsin. All the inhibitors have a novel lactam moiety at the P3 position, while the two with greatest trypsin selectivity have a guanidinopiperidyl, group at the P1 position that binds in the S1 specificity site., Differences in the binding constants of these inhibitors are correlated, with their interactions with thrombin and trypsin. The kinetics of, inhibition vary from slow to fast with thrombin and are fast in all cases, with trypsin. The kinetics are examined in terms of the slow formation of, a stable transition-state complex in a two-step mechanism. The structures, of both thrombin and trypsin complexes show similar well-defined, transition states in the S1 site and at the electrophilic carbon atom and, Ser195OG. The trypsin structures, however, suggest that the first step in, a two-step kinetic mechanism may involve formation of a weak, transition-state complex, rather than binding dominated by the P2-P4, positions.
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<StructureSection load='1bb0' size='340' side='right'caption='[[1bb0]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bb0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Hirudo_medicinalis Hirudo medicinalis] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BB0 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0IV:2-{(3S)-3-[(BENZYLSULFONYL)AMINO]-2-OXOPIPERIDIN-1-YL}-N-{(2S)-1-[(3R)-1-CARBAMIMIDOYLPIPERIDIN-3-YL]-3-OXOPROPAN-2-YL}ACETAMIDE'>0IV</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYS:O-SULFO-L-TYROSINE'>TYS</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bb0 OCA], [https://pdbe.org/1bb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bb0 RCSB], [https://www.ebi.ac.uk/pdbsum/1bb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bb0 ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Defects in F2 are the cause of factor II deficiency (FA2D) [MIM:[https://omim.org/entry/613679 613679]. It is a very rare blood coagulation disorder characterized by mucocutaneous bleeding symptoms. The severity of the bleeding manifestations correlates with blood factor II levels.<ref>PMID:14962227</ref> <ref>PMID:6405779</ref> <ref>PMID:3771562</ref> <ref>PMID:3567158</ref> <ref>PMID:3801671</ref> <ref>PMID:3242619</ref> <ref>PMID:2719946</ref> <ref>PMID:1354985</ref> <ref>PMID:1421398</ref> <ref>PMID:1349838</ref> <ref>PMID:7865694</ref> <ref>PMID:7792730</ref> Genetic variations in F2 may be a cause of susceptibility to ischemic stroke (ISCHSTR) [MIM:[https://omim.org/entry/601367 601367]; also known as cerebrovascular accident or cerebral infarction. A stroke is an acute neurologic event leading to death of neural tissue of the brain and resulting in loss of motor, sensory and/or cognitive function. Ischemic strokes, resulting from vascular occlusion, is considered to be a highly complex disease consisting of a group of heterogeneous disorders with multiple genetic and environmental risk factors.<ref>PMID:15534175</ref> Defects in F2 are the cause of thrombophilia due to thrombin defect (THPH1) [MIM:[https://omim.org/entry/188050 188050]. It is a multifactorial disorder of hemostasis characterized by abnormal platelet aggregation in response to various agents and recurrent thrombi formation. Note=A common genetic variation in the 3-prime untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increased risk of venous thrombosis. Defects in F2 are associated with susceptibility to pregnancy loss, recurrent, type 2 (RPRGL2) [MIM:[https://omim.org/entry/614390 614390]. A common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.<ref>PMID:11506076</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/THRB_HUMAN THRB_HUMAN] Thrombin, which cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII, XIII, and, in complex with thrombomodulin, protein C. Functions in blood homeostasis, inflammation and wound healing.<ref>PMID:2856554</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bb/1bb0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bb0 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structures of three highly potent and selective low-molecular weight rigid peptidyl aldehyde inhibitors complexed with thrombin have been determined and refined to R values 0.152-0. 170 at 1.8-2.1 A resolution. Since the selectivity of two of the inhibitors was &gt;1600 with respect to trypsin, the structures of trypsin-inhibited complexes of these inhibitors were also determined (R = 0.142-0.157 at 1.9-2.1 A resolution). The selectivity appears to reside in the inability of a benzenesulfonamide group to bind at the equivalent of the D-enantiomorphic S3 site of thrombin, which may be related to the lack of a 60-insertion loop in trypsin. All the inhibitors have a novel lactam moiety at the P3 position, while the two with greatest trypsin selectivity have a guanidinopiperidyl group at the P1 position that binds in the S1 specificity site. Differences in the binding constants of these inhibitors are correlated with their interactions with thrombin and trypsin. The kinetics of inhibition vary from slow to fast with thrombin and are fast in all cases with trypsin. The kinetics are examined in terms of the slow formation of a stable transition-state complex in a two-step mechanism. The structures of both thrombin and trypsin complexes show similar well-defined transition states in the S1 site and at the electrophilic carbon atom and Ser195OG. The trypsin structures, however, suggest that the first step in a two-step kinetic mechanism may involve formation of a weak transition-state complex, rather than binding dominated by the P2-P4 positions.
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==About this Structure==
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Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.,Krishnan R, Zhang E, Hakansson K, Arni RK, Tulinsky A, Lim-Wilby MS, Levy OE, Semple JE, Brunck TK Biochemistry. 1998 Sep 1;37(35):12094-103. PMID:9724521<ref>PMID:9724521</ref>
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1BB0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NA, PMS and NVA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] Structure known Active Site: CAT. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BB0 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes., Krishnan R, Zhang E, Hakansson K, Arni RK, Tulinsky A, Lim-Wilby MS, Levy OE, Semple JE, Brunck TK, Biochemistry. 1998 Sep 1;37(35):12094-103. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9724521 9724521]
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 1bb0" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Thrombin]]
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[[Category: Arni, R.K.]]
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[[Category: Brunck, T.K.]]
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[[Category: Hakansson, K.]]
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[[Category: Krishnan, R.]]
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[[Category: Levy, O.E.]]
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[[Category: Lim-Wilby, M.S.L.]]
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[[Category: Semple, J.E.]]
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[[Category: Tulinsky, A.]]
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[[Category: Zhang, E.]]
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[[Category: NA]]
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[[Category: NVA]]
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[[Category: PMS]]
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[[Category: complex (serine protease/inhibitor)]]
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[[Category: hydrolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 14:55:03 2007''
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==See Also==
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*[[Hirudin 3D structures|Hirudin 3D structures]]
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*[[Thrombin 3D Structures|Thrombin 3D Structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Hirudo medicinalis]]
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Arni RK]]
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[[Category: Brunck TK]]
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[[Category: Hakansson K]]
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[[Category: Krishnan R]]
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[[Category: Levy OE]]
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[[Category: Lim-Wilby MSL]]
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[[Category: Semple JE]]
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[[Category: Tulinsky A]]
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[[Category: Zhang E]]

Current revision

THROMBIN INHIBITORS WITH RIGID TRIPEPTIDYL ALDEHYDES

PDB ID 1bb0

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