5jmw - Revision history

OCA at 18:59, 20 September 2023

OCA — Wed, 20 Sep 2023 18:59:03 GMT

←Older revision		Revision as of 18:59, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jmw' size='340' side='right'caption='[[5jmw]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5jmw' size='340' side='right'caption='[[5jmw]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jmw]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Plaf7 Plaf7~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JMW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jmw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JMW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L50:[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHYLPHENYL)PENTYL]PHOSPHONIC+ACID'>L50</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.55Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DXR, PF14_0641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36329 PLAF7])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L50:[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHYLPHENYL)PENTYL]PHOSPHONIC+ACID'>L50</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=5jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmw OCA], [https://pdbe.org/5jmw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jmw RCSB], [https://www.ebi.ac.uk/pdbsum/5jmw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmw ProSAT]</span></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=5jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmw OCA], [~~http~~://pdbe.org/5jmw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jmw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jmw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DXR_PLAF7 DXR_PLAF7]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).	+	[https://www.uniprot.org/uniprot/DXR_PLAF7 DXR_PLAF7] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[DXP reductoisomerase\|DXP reductoisomerase]]	+	*[[DXP reductoisomerase 3D Structures\|DXP reductoisomerase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Plaf7~~]]	+	[[Category: Plasmodium falciparum 3D7]]
-	[[Category: Bergfors, T]]	+	[[Category: Bergfors T]]
-	[[Category: Jones~~, T A~~]]	+	[[Category: Jones TA]]
-	[[Category: Mowbray~~, S L~~]]	+	[[Category: Mowbray SL]]
-	[[Category: Sooriyaarachchi, S]]	+	[[Category: Sooriyaarachchi S]]
-	~~[[Category: Enzyme-inhibitor complex]]~~	+
-	~~[[Category: Isoprenoid biosynthesis]]~~	+
-	~~[[Category: Mep pathway]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:55, 10 June 2020

OCA — Wed, 10 Jun 2020 07:55:54 GMT

←Older revision		Revision as of 07:55, 10 June 2020
Line 1:		Line 1:

	==Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese==		==Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese==
-	<StructureSection load='5jmw' size='340' side='right' caption='[[5jmw]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5jmw' size='340' side='right'caption='[[5jmw]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jmw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMW OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JMW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jmw]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Plaf7 Plaf7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JMW FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L50:[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHYLPHENYL)PENTYL]PHOSPHONIC+ACID'>L50</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L50:[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHYLPHENYL)PENTYL]PHOSPHONIC+ACID'>L50</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DXR, PF14_0641 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=36329 PLAF7])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=5jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmw OCA], [http://pdbe.org/5jmw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmw RCSB], [http://www.ebi.ac.uk/pdbsum/5jmw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmw ProSAT]</span></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=5jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmw OCA], [http://pdbe.org/5jmw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmw RCSB], [http://www.ebi.ac.uk/pdbsum/5jmw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmw ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5jmw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jmw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DXP reductoisomerase\|DXP reductoisomerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Plaf7]]
	[[Category: Bergfors, T]]		[[Category: Bergfors, T]]
	[[Category: Jones, T A]]		[[Category: Jones, T A]]

OCA at 06:52, 10 September 2016

OCA — Sat, 10 Sep 2016 06:52:39 GMT

←Older revision		Revision as of 06:52, 10 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jmw is ~~ON HOLD~~	+	==Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese==
		+	<StructureSection load='5jmw' size='340' side='right' caption='[[5jmw]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jmw]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JMW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JMW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=L50:[(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5-(4-METHYLPHENYL)PENTYL]PHOSPHONIC+ACID'>L50</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=5jmw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jmw OCA], [http://pdbe.org/5jmw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jmw RCSB], [http://www.ebi.ac.uk/pdbsum/5jmw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jmw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DXR_PLAF7 DXR_PLAF7]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Blocking the 2-C-methyl-d-erythrithol-4-phosphate pathway for isoprenoid biosynthesis offers new ways to inhibit the growth of Plasmodium spp. Fosmidomycin [(3-(N-hydroxyformamido)propyl)phosphonic acid, 1] and its acetyl homologue FR-900098 [(3-(N-hydroxyacetamido)propyl)phosphonic acid, 2] potently inhibit 1-deoxy-d-xylulose-5-phosphate reductoisomerase (Dxr), a key enzyme in this biosynthetic pathway. Arylpropyl substituents were introduced at the beta-position of the hydroxamate analogue of 2 to study changes in lipophilicity, as well as electronic and steric properties. The potency of several new compounds on the P. falciparum enzyme approaches that of 1 and 2. Activities against the enzyme and parasite correlate well, supporting the mode of action. Seven X-ray structures show that all of the new arylpropyl substituents displace a key tryptophan residue of the active-site flap, which had made favorable interactions with 1 and 2. Plasticity of the flap allows substituents to be accommodated in many ways; in most cases, the flap is largely disordered. Compounds can be separated into two classes based on whether the substituent on the aromatic ring is at the meta or para position. Generally, meta-substituted compounds are better inhibitors, and in both classes, smaller size is linked to better potency.

-	~~Authors: Sooriyaarachchi~~, S., ~~Bergfors~~, T., ~~Jones~~, ~~T.A.~~, ~~Mowbray~~, S.L.	+	Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin.,Sooriyaarachchi S, Chofor R, Risseeuw MD, Bergfors T, Pouyez J, Dowd CS, Maes L, Wouters J, Jones TA, Van Calenbergh S, Mowbray SL ChemMedChem. 2016 Aug 3. doi: 10.1002/cmdc.201600249. PMID:27487410<ref>PMID:27487410</ref>

-	~~Description: Structure of Plasmodium falciparum DXR in complex with~~ a ~~beta~~-~~substituted fosmidomycin analogue, LC50 and manganese~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jmw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Bergfors, T]]		[[Category: Bergfors, T]]
-	[[Category: Jones, T.A]]	+	[[Category: Jones, T A]]
-	[[Category: Mowbray, S.L]]	+	[[Category: Mowbray, S L]]
	[[Category: Sooriyaarachchi, S]]		[[Category: Sooriyaarachchi, S]]
		+	[[Category: Enzyme-inhibitor complex]]
		+	[[Category: Isoprenoid biosynthesis]]
		+	[[Category: Mep pathway]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5jmw" [edit=sysop:move=sysop]

OCA — Sun, 15 May 2016 15:36:14 GMT

Protected "5jmw" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:36, 15 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jmw is ON HOLD Authors: Sooriyaarachchi, S., Bergfors, T., Jones, T.A., Mowbray, S.L. Description: Structure of Plasmodium falciparum DXR in compl...

OCA — Sun, 15 May 2016 15:36:13 GMT

New page: '''Unreleased structure''' The entry 5jmw is ON HOLD Authors: Sooriyaarachchi, S., Bergfors, T., Jones, T.A., Mowbray, S.L. Description: Structure of Plasmodium falciparum DXR in compl...

New page

'''Unreleased structure'''

The entry 5jmw is ON HOLD

Authors: Sooriyaarachchi, S., Bergfors, T., Jones, T.A., Mowbray, S.L.

Description: Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese
[[Category: Unreleased Structures]]
[[Category: Bergfors, T]]
[[Category: Jones, T.A]]
[[Category: Mowbray, S.L]]
[[Category: Sooriyaarachchi, S]]