3rda - Revision history

OCA at 12:19, 14 March 2024

2024-03-14T12:19:21Z

← Older revision		Revision as of 12:19, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3rda' size='340' side='right'caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>		<StructureSection load='3rda' size='340' side='right'caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rda]] 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=3RDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDA FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MIO:3~~-~~METHYL-1~~,~~2-OXAZOL-5-AMINE'>MIO</scene></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.07Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; max-height: 3em;'>[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</div></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PPIF, CYP3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~
	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase]~~, ~~with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=~~5~~.2.1.8 5.2.1.8]~~ </~~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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [https://pdbe.org/3rda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [https://www.ebi.ac.uk/pdbsum/3rda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rda 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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [https://pdbe.org/3rda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [https://www.ebi.ac.uk/pdbsum/3rda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rda ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>		[https://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Cyclophilins are peptidyl-prolyl cis/trans isomerases (PPIase) that catalyse the interconversion of the peptide bond at proline residues. Several cyclophilins play a pivotal role in the life cycle of a number of viruses. The existing cyclophilin inhibitors, all derived from cyclosporine A or sanglifehrin A, have disadvantages, including their size, potential for side effects unrelated to cyclophilin inhibition and drug-drug interactions, unclear antiviral spectrum and manufacturing issues. Here we use a fragment-based drug discovery approach using nucleic magnetic resonance, X-ray crystallography and structure-based compound optimization to generate a new family of non-peptidic, small-molecule cyclophilin inhibitors with potent in vitro PPIase inhibitory activity and antiviral activity against hepatitis C virus, human immunodeficiency virus and coronaviruses. This family of compounds has the potential for broad-spectrum, high-barrier-to-resistance treatment of viral infections.

	Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.,Ahmed-Belkacem A, Colliandre L, Ahnou N, Nevers Q, Gelin M, Bessin Y, Brillet R, Cala O, Douguet D, Bourguet W, Krimm I, Pawlotsky JM, Guichou JF Nat Commun. 2016 Sep 22;7:12777. doi: 10.1038/ncomms12777. PMID:27652979<ref>PMID:27652979</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3rda" style="background-color:#fffaf0;"></div~~>

	==See Also==		==See Also==
Line 28:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Peptidylprolyl isomerase]]~~		[[Category: Ahmed-Belkacem H]]
	[[Category: Ahmed-Belkacem, H]]		[[Category: Bessin Y]]
	[[Category: Bessin, Y]]		[[Category: Colliandre L]]
	[[Category: Colliandre, L]]		[[Category: Guichou JF]]
	[[Category: Guichou~~, J F~~]]		[[Category: Pawlotsky JM]]
	[[Category: Pawlotsky~~, J M]]~~
	~~[[Category: Beta barrel]]~~
	~~[[Category: Inhibitor]]~~
	~~[[Category: Isomerase-isomerase inhibitor complex]]~~
	~~[[Category: Mitochondria]]~~
	~~[[Category: Prolyl cis/trans isomerase~~]]

OCA at 05:58, 15 June 2022

2022-06-15T05:58:46Z

← Older revision		Revision as of 05:58, 15 June 2022
Line 1:		Line 1:

	==Human Cyclophilin D Complexed with a Fragment==		==Human Cyclophilin D Complexed with a Fragment==
	<StructureSection load='3rda' size='340' side='right' caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>		<StructureSection load='3rda' size='340' side='right'caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rda]] 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=3RDA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RDA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rda]] 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=3RDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [~~http~~://pdbe.org/3rda PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rda PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rda 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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [https://pdbe.org/3rda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [https://www.ebi.ac.uk/pdbsum/3rda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rda ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>		[[https://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
	*[[Cyclophilin\|Cyclophilin]]		*[[Cyclophilin 3D structures\|Cyclophilin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Ahmed-Belkacem, H]]		[[Category: Ahmed-Belkacem, H]]

OCA at 09:17, 19 October 2016

2016-10-19T09:17:39Z

← Older revision		Revision as of 09:17, 19 October 2016
Line 12:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>		[[http://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Cyclophilins are peptidyl-prolyl cis/trans isomerases (PPIase) that catalyse the interconversion of the peptide bond at proline residues. Several cyclophilins play a pivotal role in the life cycle of a number of viruses. The existing cyclophilin inhibitors, all derived from cyclosporine A or sanglifehrin A, have disadvantages, including their size, potential for side effects unrelated to cyclophilin inhibition and drug-drug interactions, unclear antiviral spectrum and manufacturing issues. Here we use a fragment-based drug discovery approach using nucleic magnetic resonance, X-ray crystallography and structure-based compound optimization to generate a new family of non-peptidic, small-molecule cyclophilin inhibitors with potent in vitro PPIase inhibitory activity and antiviral activity against hepatitis C virus, human immunodeficiency virus and coronaviruses. This family of compounds has the potential for broad-spectrum, high-barrier-to-resistance treatment of viral infections.

			Fragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities.,Ahmed-Belkacem A, Colliandre L, Ahnou N, Nevers Q, Gelin M, Bessin Y, Brillet R, Cala O, Douguet D, Bourguet W, Krimm I, Pawlotsky JM, Guichou JF Nat Commun. 2016 Sep 22;7:12777. doi: 10.1038/ncomms12777. PMID:27652979<ref>PMID:27652979</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 3rda" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 13:37, 5 August 2016

2016-08-05T13:37:14Z

← Older revision		Revision as of 13:37, 5 August 2016
Line 1:		Line 1:

	==Human Cyclophilin D Complexed with a Fragment==		==Human Cyclophilin D Complexed with a Fragment==
	<StructureSection load='3rda' size='340' side='right' caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>		<StructureSection load='3rda' size='340' side='right' caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rda]] 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=3RDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [http://www.ebi.ac.uk/pdbsum/3rda PDBsum]</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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [http://pdbe.org/3rda PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [http://www.ebi.ac.uk/pdbsum/3rda PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rda ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Ahmed-Belkacem, H]]		[[Category: Ahmed-Belkacem, H]]

OCA at 02:56, 25 December 2014

2014-12-25T02:56:02Z

← Older revision		Revision as of 02:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDA FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDA FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [http://www.ebi.ac.uk/pdbsum/3rda PDBsum]</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=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [http://www.ebi.ac.uk/pdbsum/3rda PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/PPIF_HUMAN PPIF_HUMAN]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probablity of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis.<ref>PMID:19228691</ref> <ref>PMID:22726440</ref>

			==See Also==
			*[[Cyclophilin\|Cyclophilin]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]
	[[Category: Ahmed-Belkacem, H.]]		[[Category: Ahmed-Belkacem, H]]
	[[Category: Bessin, Y.]]		[[Category: Bessin, Y]]
	[[Category: Colliandre, L.]]		[[Category: Colliandre, L]]
	[[Category: Guichou, J F.]]		[[Category: Guichou, J F]]
	[[Category: Pawlotsky, J M.]]		[[Category: Pawlotsky, J M]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Inhibitor]]		[[Category: Inhibitor]]

OCA at 04:39, 5 June 2014

2014-06-05T04:39:20Z

← Older revision		Revision as of 04:39, 5 June 2014
Line 1:		Line 1:
	~~[[Image:3rda.jpg\|left\|200px]]~~		==Human Cyclophilin D Complexed with a Fragment==
			<StructureSection load='3rda' size='340' side='right' caption='[[3rda]], [[Resolution\|resolution]] 1.07Å' scene=''>
	~~<!--~~		== Structural highlights ==
	~~The line below this paragraph, containing "STRUCTURE_3rda", creates the "Structure Box" on the page.~~		<table><tr><td colspan='2'>[[3rda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDA FirstGlance]. <br>
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MIO:3-METHYL-1,2-OXAZOL-5-AMINE'>MIO</scene><br>
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r49\|3r49]], [[3r4g\|3r4g]], [[3r54\|3r54]], [[3r56\|3r56]], [[3r57\|3r57]], [[3r59\|3r59]], [[3rcf\|3rcf]], [[3rcg\|3rcg]], [[3rci\|3rci]], [[3rck\|3rck]], [[3rcl\|3rcl]], [[3rd9\|3rd9]], [[3rdb\|3rdb]], [[3rdc\|3rdc]], [[3rdd\|3rdd]]</td></tr>
	~~or leave the SCENE parameter empty for the default display.~~		<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PPIF, CYP3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	~~-->~~		<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </span></td></tr>
	~~{{STRUCTURE_3rda\| PDB=3rda \| SCENE= }}~~		<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rda OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rda RCSB], [http://www.ebi.ac.uk/pdbsum/3rda PDBsum]</span></td></tr>
			<table>
	===Human Cyclophilin D Complexed with a Fragment===		__TOC__
			</StructureSection>

	==~~About this Structure~~==
	[[3rda]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDA OCA].
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Peptidylprolyl isomerase]]		[[Category: Peptidylprolyl isomerase]]

OCA at 07:44, 21 March 2012

2012-03-21T07:44:41Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:3rda.jpg|left|200px]]
-The entry 3rda is ON HOLD  until Paper Publication
+<!--
-Authors: Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.
+===Human Cyclophilin D Complexed with a Fragment===
-Description: Human Cyclophilin D Complexed with a Fragment

OCA: Protected "3rda" [edit=sysop:move=sysop]

2011-04-13T04:58:45Z

Protected "3rda" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:58, 13 April 2011
(No difference)

OCA: New page: '''Unreleased structure''' The entry 3rda is ON HOLD until Paper Publication Authors: Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F. Description: Human ...

2011-04-13T04:58:45Z

New page: '''Unreleased structure''' The entry 3rda is ON HOLD until Paper Publication Authors: Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F. Description: Human ...

New page

'''Unreleased structure'''

The entry 3rda is ON HOLD until Paper Publication

Authors: Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.

Description: Human Cyclophilin D Complexed with a Fragment