This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


6dmj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:35, 13 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6dmj' size='340' side='right'caption='[[6dmj]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
<StructureSection load='6dmj' size='340' side='right'caption='[[6dmj]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6dmj]] 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=6DMJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DMJ FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6dmj]] 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=6DMJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DMJ FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=53W:5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2-[2-(4-METHOXYPHENYL)ETHYL]-1-[2-(MORPHOLIN-4-YL)ETHYL]-1H-BENZIMIDAZOLE'>53W</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]] 1.15&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5cfw|5cfw]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=53W:5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2-[2-(4-METHOXYPHENYL)ETHYL]-1-[2-(MORPHOLIN-4-YL)ETHYL]-1H-BENZIMIDAZOLE'>53W</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BRD4, HUNK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dmj OCA], [https://pdbe.org/6dmj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dmj RCSB], [https://www.ebi.ac.uk/pdbsum/6dmj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dmj ProSAT]</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=6dmj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dmj OCA], [http://pdbe.org/6dmj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dmj RCSB], [http://www.ebi.ac.uk/pdbsum/6dmj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dmj ProSAT]</span></td></tr>
+
</table>
</table>
== Disease ==
== Disease ==
-
[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>
+
[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Note=A chromosomal aberration involving BRD4 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;19)(q14;p13) with NUT which produces a BRD4-NUT fusion protein.<ref>PMID:12543779</ref> <ref>PMID:11733348</ref>
== Function ==
== Function ==
-
[[http://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN]] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
+
[https://www.uniprot.org/uniprot/BRD4_HUMAN BRD4_HUMAN] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively iso-energetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multi-temperature crystallography could therefore augment the structure-based drug design toolbox.
+
-
 
+
-
qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.,van Zundert G, Hudson BM, de Oliveira S, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser J, van den Bedem H J Med Chem. 2018 Nov 20. doi: 10.1021/acs.jmedchem.8b01292. PMID:30457858<ref>PMID:30457858</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6dmj" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
 +
*[[CREB-binding protein 3D structures|CREB-binding protein 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Human]]
+
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Bedem, H van den]]
+
[[Category: Borrelli K]]
-
[[Category: Borrelli, K]]
+
[[Category: Day T]]
-
[[Category: Day, T]]
+
[[Category: Fonseca R]]
-
[[Category: Fonseca, R]]
+
[[Category: Fraser JS]]
-
[[Category: Fraser, J S]]
+
[[Category: Heliou A]]
-
[[Category: Heliou, A]]
+
[[Category: Hudson BM]]
-
[[Category: Hudson, B M]]
+
[[Category: Keedy D]]
-
[[Category: Keedy, D]]
+
[[Category: Suresh P]]
-
[[Category: Suresh, P]]
+
[[Category: Van Zundert G]]
-
[[Category: Zundert, G van]]
+
[[Category: Van den Bedem H]]
-
[[Category: Complex]]
+
-
[[Category: Inhibitor]]
+
-
[[Category: Multiconformer model]]
+
-
[[Category: Transcription]]
+
-
[[Category: Transcription-transcription inhibitor complex]]
+

Current revision

A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain

PDB ID 6dmj

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dmj"
Personal tools