6wwb

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the second bromodomain of human BRD2 in complex with the compound 3b

Structural highlights

6wwb is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.31Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BRD2_HUMAN May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.^[1]

Publication Abstract from PubMed

Targeting cereblon (CRBN) is currently one of the most frequently reported proteolysis-targeting chimera (PROTAC) approaches, owing to favorable drug-like properties of CRBN ligands, immunomodulatory imide drugs (IMiDs). However, IMiDs are known to be inherently unstable, readily undergoing hydrolysis in body fluids. Here we show that IMiDs and IMiD-based PROTACs rapidly hydrolyze in commonly utilized cell media, which significantly affects their cell efficacy. We designed novel CRBN binders, phenyl glutarimide (PG) analogues, and showed that they retained affinity for CRBN with high ligand efficiency (LE >0.48) and displayed improved chemical stability. Our efforts led to the discovery of PG PROTAC 4c (SJ995973), a uniquely potent degrader of bromodomain and extra-terminal (BET) proteins that inhibited the viability of human acute myeloid leukemia MV4-11 cells at low picomolar concentrations (IC 50 = 3 pM; BRD4 DC 50 = 0.87 nM). These findings strongly support the utility of PG derivatives in the design of CRBN-directed PROTACs.

Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs.,Rankovic Z, Min J, Mayasundari A, Keramatnia F, Jonchere B, Yang SW, Jarusiewicz JA, Actis M, Das S, Young BM, Slavish PJ, Yang L, Li Y, Fu X, Garrett SH, Yun MK, Li Z, Nithianantham S, Chai SC, Chen T, Shelat AA, Lee RE, Nishiguchi G, White SW, Roussel MF, Potts PR, Fischer M Angew Chem Int Ed Engl. 2021 Oct 6. doi: 10.1002/anie.202108848. PMID:34614283^[2]

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

References

↑ LeRoy G, Rickards B, Flint SJ. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol Cell. 2008 Apr 11;30(1):51-60. doi: 10.1016/j.molcel.2008.01.018. PMID:18406326 doi:10.1016/j.molcel.2008.01.018
↑ Rankovic Z, Min J, Mayasundari A, Keramatnia F, Jonchere B, Yang SW, Jarusiewicz JA, Actis M, Das S, Young BM, Slavish PJ, Yang L, Li Y, Fu X, Garrett SH, Yun MK, Li Z, Nithianantham S, Chai SC, Chen T, Shelat AA, Lee RE, Nishiguchi G, White SW, Roussel MF, Potts PR, Fischer M. Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs. Angew Chem Int Ed Engl. 2021 Oct 6. doi: 10.1002/anie.202108848. PMID:34614283 doi:http://dx.doi.org/10.1002/anie.202108848

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6wwb"

Categories: Homo sapiens | Large Structures | White SW | Yun M

@@ Line 3: / Line 3: @@
 <StructureSection load='6wwb' size='340' side='right'caption='[[6wwb]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6wwb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WWB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6wwb]] 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=6WWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WWB 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=YA3:2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)-N-((1-(4-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)acetamido)butyl)-1H-1,2,3-triazol-4-yl)methyl)acetamide'>YA3</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]] 1.31&#8491;</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=YA3:2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)-N-((1-(4-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)acetamido)butyl)-1H-1,2,3-triazol-4-yl)methyl)acetamide'>YA3</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=6wwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wwb OCA], [https://pdbe.org/6wwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wwb RCSB], [https://www.ebi.ac.uk/pdbsum/6wwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wwb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN]] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
+[https://www.uniprot.org/uniprot/BRD2_HUMAN BRD2_HUMAN] May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly.<ref>PMID:18406326</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: White, S W]]
+[[Category: White SW]]
-[[Category: Yun, M]]
+[[Category: Yun M]]
-[[Category: Bet]]
-[[Category: Brd2]]
-[[Category: Bromodomain]]
-[[Category: Complex]]
-[[Category: Inhibitor]]
-[[Category: Protac]]
-[[Category: Transcription]]

6wwb

From Proteopedia

Current revision

Crystal Structure of the second bromodomain of human BRD2 in complex with the compound 3b

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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