6tbx - Revision history

OCA at 12:59, 24 January 2024

2024-01-24T12:59:18Z

←Older revision		Revision as of 12:59, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tbx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Trybb Trybb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tbx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>
-	</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N0Z:2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol'>N0Z</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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]] 1.3Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></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=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N0Z:2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol'>N0Z</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTR1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])~~</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=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [https://pdbe.org/6tbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [https://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx 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=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [https://pdbe.org/6tbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [https://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O76290_TRYBB O76290_TRYBB]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Trybb~~]]	+	[[Category: Trypanosoma brucei brucei]]
-	[[Category: Landi, G]]	+	[[Category: Landi G]]
-	[[Category: Mangani, S]]	+	[[Category: Mangani S]]
-	[[Category: Pozzi, C]]	+	[[Category: Pozzi C]]
-	[[Category: Tassone, G]]	+	[[Category: Tassone G]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pteridine reductase]]~~	+
-	~~[[Category: Tbptr1]]~~	+
-	~~[[Category: Tricyclic based inhibitor]]~~	+
-	~~[[Category: Trypanosoma brucei~~]]	+

OCA at 15:18, 8 June 2021

2021-06-08T15:18:29Z

←Older revision		Revision as of 15:18, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]], [[Resolution\|resolution]] 1.30Å' scene=''>		<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tbx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tbx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>
	</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N0Z:2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol'>N0Z</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N0Z:2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol'>N0Z</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTR1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTR1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [~~http~~://pdbe.org/6tbx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx 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=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [https://pdbe.org/6tbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [https://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 6tbx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tbx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Pteridine reductase\|Pteridine reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:38, 17 June 2020

2020-06-17T10:38:21Z

←Older revision		Revision as of 10:38, 17 June 2020
Line 1:		Line 1:

	==Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor==		==Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor==
-	<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]]' scene=''>	+	<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]], [[Resolution\|resolution]] 1.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tbx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [http://pdbe.org/6tbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [http://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx ProSAT]</span></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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=N0Z:2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol'>N0Z</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PTR1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [http://pdbe.org/6tbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [http://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The protozoan parasite Trypanosoma brucei is the etiological agent of human African trypanosomiasis (HAT). HAT, together with other neglected tropical diseases, causes serious health and economic issues, especially in tropical and subtropical areas. The classical antifolates targeting dihydrofolate reductase (DHFR) are ineffective towards trypanosomatid parasites owing to a metabolic bypass by the expression of pteridine reductase 1 (PTR1). The combined inhibition of PTR1 and DHFR activities in Trypanosoma parasites represents a promising strategy for the development of new effective treatments for HAT. To date, only monocyclic and bicyclic aromatic systems have been proposed as inhibitors of T. brucei PTR1 (TbPTR1); nevertheless, the size of the catalytic cavity allows the accommodation of expanded molecular cores. Here, an innovative tricyclic-based compound has been explored as a TbPTR1-targeting molecule and its potential application for the development of a new class of PTR1 inhibitors has been evaluated. 2,4-Diaminopyrimido[4,5-b]indol-6-ol (1) was designed and synthesized, and was found to be effective in blocking TbPTR1 activity, with a Ki in the low-micromolar range. The binding mode of 1 was clarified through the structural characterization of its ternary complex with TbPTR1 and the cofactor NADP(H), which was determined to 1.30 A resolution. The compound adopts a substrate-like orientation inside the cavity that maximizes the binding contributions of hydrophobic and hydrogen-bond interactions. The binding mode of 1 was compared with those of previously reported bicyclic inhibitors, providing new insights for the design of innovative tricyclic-based molecules targeting TbPTR1.
		+
		+	High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor.,Landi G, Linciano P, Tassone G, Costi MP, Mangani S, Pozzi C Acta Crystallogr D Struct Biol. 2020 Jun 1;76(Pt 6):558-564. doi:, 10.1107/S2059798320004891. Epub 2020 May 29. PMID:32496217<ref>PMID:32496217</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tbx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Landi, G, ~~Tassone, G,~~ Pozzi, C, ~~Mangani, S~~]]	+	[[Category: Trybb]]
		+	[[Category: Landi, G]]
		+	[[Category: Mangani, S]]
		+	[[Category: Pozzi, C]]
		+	[[Category: Tassone, G]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pteridine reductase]]
		+	[[Category: Tbptr1]]
		+	[[Category: Tricyclic based inhibitor]]
		+	[[Category: Trypanosoma brucei]]

OCA at 06:27, 3 June 2020

2020-06-03T06:27:57Z

←Older revision		Revision as of 06:27, 3 June 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6tbx is ON HOLD until Paper Publication~~	+	==Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor==
-		+	<StructureSection load='6tbx' size='340' side='right'caption='[[6tbx]]' scene=''>
-	~~Authors: Landi, G., Tassone, G., Pozzi, C., Mangani, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TBX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TBX FirstGlance]. <br>
-	~~Description:~~ Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6tbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tbx OCA], [http://pdbe.org/6tbx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tbx RCSB], [http://www.ebi.ac.uk/pdbsum/6tbx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tbx ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Landi, G]~~]	+	__TOC__
-	[[~~Category~~: ~~Mangani~~, S]]	+	</StructureSection>
-	[[Category: ~~Tassone, G~~]]	+	[[Category: Large Structures]]
-	[[Category: Pozzi, C]]	+	[[Category: Landi, G, Tassone, G, Pozzi, C, Mangani, S]]

OCA: Protected "6tbx" [edit=sysop:move=sysop]

2019-11-13T09:27:21Z

Protected "6tbx" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:27, 13 November 2019

OCA: New page: '''Unreleased structure''' The entry 6tbx is ON HOLD until Paper Publication Authors: Landi, G., Tassone, G., Pozzi, C., Mangani, S. Description: Trypanosoma brucei PTR1 (TbPTR1) in co...

2019-11-13T09:27:19Z

New page: '''Unreleased structure''' The entry 6tbx is ON HOLD until Paper Publication Authors: Landi, G., Tassone, G., Pozzi, C., Mangani, S. Description: Trypanosoma brucei PTR1 (TbPTR1) in co...

New page

'''Unreleased structure'''

The entry 6tbx is ON HOLD until Paper Publication

Authors: Landi, G., Tassone, G., Pozzi, C., Mangani, S.

Description: Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor
[[Category: Unreleased Structures]]
[[Category: Landi, G]]
[[Category: Mangani, S]]
[[Category: Tassone, G]]
[[Category: Pozzi, C]]