2vip

From Proteopedia

(Difference between revisions)

Revision as of 10:46, 7 July 2021

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator

Structural highlights

2vip is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2viv, 1c5x, 1gj9, 2vio, 1w0z, 1fv9, 1vja, 1gj8, 1w11, 1sqo, 1gjd, 1w10, 1owk, 1w12, 1gi9, 1o5a, 1c5z, 1owj, 1gi7, 1o5b, 1gjc, 1sc8, 1gja, 1o3p, 1owe, 1sqa, 1gjb, 2viw, 1f92, 1owi, 1kdu, 2vin, 1sqt, 1f5l, 1owd, 1ejn, 2viq, 1lmw, 1u6q, 1gi8, 2jde, 1c5y, 1w14, 1vj9, 1w13, 1gj7, 1c5w, 1owh, 1o5c
Activity:	U-plasminogen activator, with EC number 3.4.21.73
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[UROK_HUMAN] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:601709]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.^[1]

Function

[UROK_HUMAN] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.

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 PubMed

Fragment-based lead discovery has been applied to urokinase-type plasminogen activator (uPA). The (R)-enantiomer of the orally active drug mexiletine 5 (a fragment hit from X-ray crystallographic screening) was the chemical starting point. Structure-aided design led to elaborated inhibitors that retained the key interactions of (R)-5 while gaining extra potency by simultaneously occupying neighboring regions of the active site. Subsequent optimization led to 15, a potent, selective, and orally bioavailable inhibitor of uPA.

Fragment-based discovery of mexiletine derivatives as orally bioavailable inhibitors of urokinase-type plasminogen activator.,Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinkovic M, Wallis NG J Med Chem. 2008 Jan 24;51(2):183-6. Epub 2007 Dec 29. PMID:18163548^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Paterson AD, Rommens JM, Bharaj B, Blavignac J, Wong I, Diamandis M, Waye JS, Rivard GE, Hayward CP. Persons with Quebec platelet disorder have a tandem duplication of PLAU, the urokinase plasminogen activator gene. Blood. 2010 Feb 11;115(6):1264-6. doi: 10.1182/blood-2009-07-233965. Epub 2009, Dec 9. PMID:20007542 doi:10.1182/blood-2009-07-233965
↑ Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinkovic M, Wallis NG. Fragment-based discovery of mexiletine derivatives as orally bioavailable inhibitors of urokinase-type plasminogen activator. J Med Chem. 2008 Jan 24;51(2):183-6. Epub 2007 Dec 29. PMID:18163548 doi:http://dx.doi.org/10.1021/jm701359z

1 Structural highlights
2 Disease
3 Function
4 Evolutionary Conservation
5 Publication Abstract from PubMed
6 See Also
7 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vip"

@@ Line 3: / Line 3: @@
 <StructureSection load='2vip' size='340' side='right'caption='[[2vip]], [[Resolution|resolution]] 1.72&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vip]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VIP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vip]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VIP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=L1R:4-(2-AMINOETHOXY)-3,5-DICHLORO-N-[3-(1-METHYLETHOXY)PHENYL]BENZAMIDE'>L1R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=L1R:4-(2-AMINOETHOXY)-3,5-DICHLORO-N-[3-(1-METHYLETHOXY)PHENYL]BENZAMIDE'>L1R</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2viv|2viv]], [[1c5x|1c5x]], [[1gj9|1gj9]], [[2vio|2vio]], [[1w0z|1w0z]], [[1fv9|1fv9]], [[1vja|1vja]], [[1gj8|1gj8]], [[1w11|1w11]], [[1sqo|1sqo]], [[1gjd|1gjd]], [[1w10|1w10]], [[1owk|1owk]], [[1w12|1w12]], [[1gi9|1gi9]], [[1o5a|1o5a]], [[1c5z|1c5z]], [[1owj|1owj]], [[1gi7|1gi7]], [[1o5b|1o5b]], [[1gjc|1gjc]], [[1sc8|1sc8]], [[1gja|1gja]], [[1o3p|1o3p]], [[1owe|1owe]], [[1sqa|1sqa]], [[1gjb|1gjb]], [[2viw|2viw]], [[1f92|1f92]], [[1owi|1owi]], [[1kdu|1kdu]], [[2vin|2vin]], [[1sqt|1sqt]], [[1f5l|1f5l]], [[1owd|1owd]], [[1ejn|1ejn]], [[2viq|2viq]], [[1lmw|1lmw]], [[1u6q|1u6q]], [[1gi8|1gi8]], [[2jde|2jde]], [[1c5y|1c5y]], [[1w14|1w14]], [[1vj9|1vj9]], [[1w13|1w13]], [[1gj7|1gj7]], [[1c5w|1c5w]], [[1owh|1owh]], [[1o5c|1o5c]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2viv|2viv]], [[1c5x|1c5x]], [[1gj9|1gj9]], [[2vio|2vio]], [[1w0z|1w0z]], [[1fv9|1fv9]], [[1vja|1vja]], [[1gj8|1gj8]], [[1w11|1w11]], [[1sqo|1sqo]], [[1gjd|1gjd]], [[1w10|1w10]], [[1owk|1owk]], [[1w12|1w12]], [[1gi9|1gi9]], [[1o5a|1o5a]], [[1c5z|1c5z]], [[1owj|1owj]], [[1gi7|1gi7]], [[1o5b|1o5b]], [[1gjc|1gjc]], [[1sc8|1sc8]], [[1gja|1gja]], [[1o3p|1o3p]], [[1owe|1owe]], [[1sqa|1sqa]], [[1gjb|1gjb]], [[2viw|2viw]], [[1f92|1f92]], [[1owi|1owi]], [[1kdu|1kdu]], [[2vin|2vin]], [[1sqt|1sqt]], [[1f5l|1f5l]], [[1owd|1owd]], [[1ejn|1ejn]], [[2viq|2viq]], [[1lmw|1lmw]], [[1u6q|1u6q]], [[1gi8|1gi8]], [[2jde|2jde]], [[1c5y|1c5y]], [[1w14|1w14]], [[1vj9|1vj9]], [[1w13|1w13]], [[1gj7|1gj7]], [[1c5w|1c5w]], [[1owh|1owh]], [[1o5c|1o5c]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </span></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/U-plasminogen_activator U-plasminogen activator], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.73 3.4.21.73] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vip OCA], [http://pdbe.org/2vip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vip RCSB], [http://www.ebi.ac.uk/pdbsum/2vip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vip ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vip OCA], [https://pdbe.org/2vip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vip RCSB], [https://www.ebi.ac.uk/pdbsum/2vip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vip ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[http://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>
+[[https://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Defects in PLAU are the cause of Quebec platelet disorder (QPD) [MIM:[https://omim.org/entry/601709 601709]]. QPD is an autosomal dominant bleeding disorder due to a gain-of-function defect in fibrinolysis. Although affected individuals do not exhibit systemic fibrinolysis, they show delayed onset bleeding after challenge, such as surgery. The hallmark of the disorder is markedly increased PLAU levels within platelets, which causes intraplatelet plasmin generation and secondary degradation of alpha-granule proteins.<ref>PMID:20007542</ref>
 == Function ==
-[[http://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
+[[https://www.uniprot.org/uniprot/UROK_HUMAN UROK_HUMAN]] Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 34: @@
 ==See Also==
-*[[Urokinase|Urokinase]]
+*[[Urokinase 3D Structures|Urokinase 3D Structures]]
 == References ==
 <references/>

2vip

From Proteopedia

Revision as of 10:46, 7 July 2021

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator

Structural highlights

Disease

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox