9tm1: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 9tm1 is ~~ON HOLD until Paper~~ Publication

==Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand==

== Structural highlights ==

<table><tr><td colspan='2'>[[9tm1]] is a 3 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=9TM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TM1 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1JWP:~{N}-[(2~{S})-3-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-1-(methylamino)-1-oxidanylidene-propan-2-yl]-6-methoxy-3~{H}-imidazo[4,5-b]pyridine-7-carboxamide'>A1JWP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=9tm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9tm1 OCA], [https://pdbe.org/9tm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9tm1 RCSB], [https://www.ebi.ac.uk/pdbsum/9tm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9tm1 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q8IB67_PLAF7 Q8IB67_PLAF7]

== Publication Abstract from PubMed ==

Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) is an established tool in drug discovery, used to characterize target engagement and conformational dynamics, and frequently used in both biopharmaceutical and small molecule drug discovery. Conventional HDX-MS experiments are performed at saturating ligand concentrations to generate a binding "footprint", where decreased solvent exchange reflects a local structural stabilization or reduced solvent accessibility upon binding. Here, we present an extended HDX-MS and HDX-MS/MS titration workflow with electron capture dissociation (ECD) fragmentation capable of estimating apparent dissociation constants (K(D)(app)) at global, peptide, and single amino acid resolution by fitting uptake-concentration relationships under EX2 exchange and Langmuir binding assumptions. The ability to determine affinity constants in a spatially resolved manner combined with the automation available in HDX-MS sample handling and data analysis enables quantitative mapping of ligand-protein interactions and provides a scalable approach for structure-activity relationship studies in drug discovery.

~~Authors:~~ McMillan, J., Postis, V.~~, Masson, G~~.

Residue-Level Determination of Small-Molecule-Protein Affinities by Hydrogen-Deuterium Exchange Mass Spectrometry.,Lin D, Magalhaes LG, McMillan J, Eadsforth TC, Stewart G, Cartmill KR, Postis VLG, Masson GR J Am Soc Mass Spectrom. 2026 Mar 31. doi: 10.1021/jasms.6c00020. PMID:41915381<ref>PMID:41915381</ref>

~~Description~~: ~~Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand~~

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

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: Masson, G]]

[[Category: ~~Mcmillan,~~ J]]

== References ==

[[Category: Postis, V]]

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Plasmodium falciparum 3D7]]

[[Category: Masson G]]

[[Category: McMillan J]]

[[Category: Postis V]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9tm1 is ON HOLD  until Paper Publication
+==Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand==
+<StructureSection load='9tm1' size='340' side='right'caption='[[9tm1]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9tm1]] is a 3 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=9TM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9TM1 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1JWP:~{N}-[(2~{S})-3-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-1-(methylamino)-1-oxidanylidene-propan-2-yl]-6-methoxy-3~{H}-imidazo[4,5-b]pyridine-7-carboxamide'>A1JWP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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=9tm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9tm1 OCA], [https://pdbe.org/9tm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9tm1 RCSB], [https://www.ebi.ac.uk/pdbsum/9tm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9tm1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8IB67_PLAF7 Q8IB67_PLAF7]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) is an established tool in drug discovery, used to characterize target engagement and conformational dynamics, and frequently used in both biopharmaceutical and small molecule drug discovery. Conventional HDX-MS experiments are performed at saturating ligand concentrations to generate a binding "footprint", where decreased solvent exchange reflects a local structural stabilization or reduced solvent accessibility upon binding. Here, we present an extended HDX-MS and HDX-MS/MS titration workflow with electron capture dissociation (ECD) fragmentation capable of estimating apparent dissociation constants (K(D)(app)) at global, peptide, and single amino acid resolution by fitting uptake-concentration relationships under EX2 exchange and Langmuir binding assumptions. The ability to determine affinity constants in a spatially resolved manner combined with the automation available in HDX-MS sample handling and data analysis enables quantitative mapping of ligand-protein interactions and provides a scalable approach for structure-activity relationship studies in drug discovery.
-Authors: McMillan, J., Postis, V., Masson, G.
+Residue-Level Determination of Small-Molecule-Protein Affinities by Hydrogen-Deuterium Exchange Mass Spectrometry.,Lin D, Magalhaes LG, McMillan J, Eadsforth TC, Stewart G, Cartmill KR, Postis VLG, Masson GR J Am Soc Mass Spectrom. 2026 Mar 31. doi: 10.1021/jasms.6c00020. PMID:41915381<ref>PMID:41915381</ref>
-Description: Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Masson, G]]
+<div class="pdbe-citations 9tm1" style="background-color:#fffaf0;"></div>
-[[Category: Mcmillan, J]]
+== References ==
-[[Category: Postis, V]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Plasmodium falciparum 3D7]]
+[[Category: Masson G]]
+[[Category: McMillan J]]
+[[Category: Postis V]]