5i88

From Proteopedia

(Difference between revisions)

Revision as of 07:08, 3 June 2020

BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)

Structural highlights

5i88 is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	5i7y
Gene:	BRD4, HUNK1 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[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.^[1] ^[2]

Function

[BRD4_HUMAN] Plays a role in a process governing chromosomal dynamics during mitosis (By similarity).

Publication Abstract from PubMed

The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.

Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains.,Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Cote A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang HR, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG J Med Chem. 2016 Jun 9;59(11):5391-402. doi: 10.1021/acs.jmedchem.6b00264. Epub, 2016 May 31. PMID:27219867^[3]

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

References

↑ French CA, Miyoshi I, Kubonishi I, Grier HE, Perez-Atayde AR, Fletcher JA. BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma. Cancer Res. 2003 Jan 15;63(2):304-7. PMID:12543779
↑ French CA, Miyoshi I, Aster JC, Kubonishi I, Kroll TG, Dal Cin P, Vargas SO, Perez-Atayde AR, Fletcher JA. BRD4 bromodomain gene rearrangement in aggressive carcinoma with translocation t(15;19). Am J Pathol. 2001 Dec;159(6):1987-92. PMID:11733348 doi:10.1016/S0002-9440(10)63049-0
↑ Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Cote A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang HR, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J Med Chem. 2016 Jun 9;59(11):5391-402. doi: 10.1021/acs.jmedchem.6b00264. Epub, 2016 May 31. PMID:27219867 doi:http://dx.doi.org/10.1021/acs.jmedchem.6b00264

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5i88"

@@ Line 1: / Line 1: @@
 ==BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)==
-<StructureSection load='5i88' size='340' side='right' caption='[[5i88]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+<StructureSection load='5i88' size='340' side='right'caption='[[5i88]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5i88]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I88 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I88 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5i88]] 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=5I88 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5I88 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=69G:3-{6-[(2E)-BUT-2-EN-1-YL]-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-C]PYRIDIN-4-YL}-N,N-DIMETHYLBENZAMIDE'>69G</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=69G:3-{6-[(2E)-BUT-2-EN-1-YL]-7-OXO-6,7-DIHYDRO-1H-PYRROLO[2,3-C]PYRIDIN-4-YL}-N,N-DIMETHYLBENZAMIDE'>69G</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5i7y|5i7y]]</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=5i88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i88 OCA], [http://pdbe.org/5i88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i88 RCSB], [http://www.ebi.ac.uk/pdbsum/5i88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i88 ProSAT]</span></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'>[http://proteopedia.org/fgij/fg.htm?mol=5i88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i88 OCA], [http://pdbe.org/5i88 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i88 RCSB], [http://www.ebi.ac.uk/pdbsum/5i88 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i88 ProSAT]</span></td></tr>
 </table>
 == Disease ==
@@ Line 21: / Line 22: @@
 </div>
 <div class="pdbe-citations 5i88" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Bromodomain-containing protein 3D structures|Bromodomain-containing protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Murray, J M]]
 [[Category: Brd4]]

5i88

From Proteopedia

Revision as of 07:08, 3 June 2020

BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide)

Structural highlights

Disease

Function

Publication Abstract from PubMed

See Also

References

Contents

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