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anti brd3 (Santa Cruz Biotechnology)

Name: anti brd3
Brand: Santa Cruz Biotechnology
Rating: 93 (44 reviews)

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Santa Cruz Biotechnology anti brd3
Anti Brd3, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 93/100, based on 44 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/anti brd3/product/Santa Cruz Biotechnology
Average 93 stars, based on 44 article reviews

anti brd3 - by Bioz Stars, 2026-02

93/100 stars

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a Structural superposition of KLHDC2 SBD (cyan, surface) bound to SJ46418 (orange, sticks) with the diGly substrate EPHB2 (chocolate, sticks, 8EBL.pdb). For clarity surface representation is depicted for the KLHDC2 SBD bound to SJ46418 only. Probable exit vectors from the ligands are depicted by arrows. Potential neo-substrate interaction surfaces with the KLHDC2 SBD U-shaped binding cleft is shown. b Chemical structure and biophysical characterization of SJ46418. Data are the average of n = 2 independent experiments. c Structural superposition of the KLHDC2 SBD (electrostatic, surface) bound to SJ46418 (orange, surface) to the diGly substrate EPHB2 (chocolate, surface, 8EBL.pdb) and the KLHDC2 targeting ligand KDRLZK1-KLHDC2 SBD (yellow, surface, 8SGE.pdb). For clarity surface electrostatic representation is depicted for KLHDC2 SBD bound to SJ46418 only. Probable exit vectors deriving from attachment sites to the ligands is depicted by arrows. d Chemical structure of JQ1 based KLHDC2 PROTAC protein degraders SJ46421 and SJ46423. e Fluorescent scan of gel monitoring SJ46421- and SJ46423-dependent ubiquitylation of the BD2 domain from BRD2, BRD3, or BRD4. Reactions were performed in pulse-chase format, with fluorescent ubiquitin charged-UBE2R2 added to neddylated CRL2 KLHDC2 and indicated PROTAC/BRD mixture. Shown is representative panels from n = 2 independent experiments. f Cartoon depiction of the biochemical assay monitoring inhibition of KLHDC2 di-Gly substrate ubiquitylation by PROTAC-mediated ternary complex formation. Briefly, neddylated CRL2 KLHDC2 was incubated with BRD3 BD2 and the indicated PROTAC prior to adding fluorescent ubiquitin-charged UBE2R2 (i.e. the pre-formed thioester-linked UBE2R2~ubiquitin intermediate) and a di-Gly protein substrate. Loss of di-Gly protein substrate ubiquitylation was quantified. g Morrison fit of data from competition ubiquitylation assay, yielding a Ki app as a measure of the strength of ternary complexes promoted by SJ46421-BRD3 BD2 and SJ46423-BRD3 BD2 . Data are the average from n = 2 independent experiments. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

doi: 10.1038/s41467-024-52966-3

Figure Lengend Snippet: a Structural superposition of KLHDC2 SBD (cyan, surface) bound to SJ46418 (orange, sticks) with the diGly substrate EPHB2 (chocolate, sticks, 8EBL.pdb). For clarity surface representation is depicted for the KLHDC2 SBD bound to SJ46418 only. Probable exit vectors from the ligands are depicted by arrows. Potential neo-substrate interaction surfaces with the KLHDC2 SBD U-shaped binding cleft is shown. b Chemical structure and biophysical characterization of SJ46418. Data are the average of n = 2 independent experiments. c Structural superposition of the KLHDC2 SBD (electrostatic, surface) bound to SJ46418 (orange, surface) to the diGly substrate EPHB2 (chocolate, surface, 8EBL.pdb) and the KLHDC2 targeting ligand KDRLZK1-KLHDC2 SBD (yellow, surface, 8SGE.pdb). For clarity surface electrostatic representation is depicted for KLHDC2 SBD bound to SJ46418 only. Probable exit vectors deriving from attachment sites to the ligands is depicted by arrows. d Chemical structure of JQ1 based KLHDC2 PROTAC protein degraders SJ46421 and SJ46423. e Fluorescent scan of gel monitoring SJ46421- and SJ46423-dependent ubiquitylation of the BD2 domain from BRD2, BRD3, or BRD4. Reactions were performed in pulse-chase format, with fluorescent ubiquitin charged-UBE2R2 added to neddylated CRL2 KLHDC2 and indicated PROTAC/BRD mixture. Shown is representative panels from n = 2 independent experiments. f Cartoon depiction of the biochemical assay monitoring inhibition of KLHDC2 di-Gly substrate ubiquitylation by PROTAC-mediated ternary complex formation. Briefly, neddylated CRL2 KLHDC2 was incubated with BRD3 BD2 and the indicated PROTAC prior to adding fluorescent ubiquitin-charged UBE2R2 (i.e. the pre-formed thioester-linked UBE2R2~ubiquitin intermediate) and a di-Gly protein substrate. Loss of di-Gly protein substrate ubiquitylation was quantified. g Morrison fit of data from competition ubiquitylation assay, yielding a Ki app as a measure of the strength of ternary complexes promoted by SJ46421-BRD3 BD2 and SJ46423-BRD3 BD2 . Data are the average from n = 2 independent experiments. Source data are provided as a Source Data file.

Article Snippet: Western blot images were obtained through detection of BRD2 (Cell Signaling D89b4 1:1000), BRD3 (Santa Cruz sc-81202 1:500), BRD4 (Cell Signaling E2A7X 1:2000), KLHDC2 (Atlas Antibodies HPA000628 1:1000), FLAG (Sigma F1804 1:1000), and GAPDH (Santa Cruz sc-32233 1:4000).

Techniques: Ubiquitin Proteomics, Chocolate, Binding Assay, Pulse Chase, Inhibition, Incubation, Ubiquitin Assay

a Thermodynamic parameters for the indicated binary and ternary complexes. Data are the average +/− 1 s.d. from n = 2 experiments. Values for ΔG and ΔH are expressed in kcal/mol −1 . b Biochemical assay monitoring inhibition of KLHDC2 diGly protein substrate ubiquitylation by PROTAC-mediated ternary complex formation, performed as in Fig. . SJ46421-BRD3 BD2 or SJ46421 alone (left panel) or SJ46423-BRD3 BD2 or SJ46423 alone (right panel) were incubated with neddylated CRL2 KLHDC2 , prior to adding fluorescent ubiquitin-charged UBE2R2 (i.e. the pre-formed thioester-linked UBE2R2~ubiquitin intermediate) and diGly protein substrate. Effective PROTAC protein degraders promote ubiquitin transfer to BRD3 BD2 neo-substrate concomitant with loss of diGly substrate ubiquitylation. Samples were reduced when reaction was quenched by addition of SDS buffer. Loss of substrate ubiquitylation was quantified. Shown is representative panels from n = 2 independent experiments. c Quantification of loss of diGly substrate ubiquitylation from the gels in panel. b Data are the average from n = 2 independent experiments. d Sequence alignment of the second bromodomain from BRD2, BRD3, and BRD4. Residue boundaries of the domains are shown, and E344 from BRD3 BD2 is highlighted in red (top panel). Superposition of BRD2 BD2 (salmon; 3ONI.pdb) and BRD3 BD2 (chocolate; 3S92.pdb) to the structure of the VHL-MZL-BRD4 BD2 ternary complex (cyan, orange, and red respectively;5T35.pdb). G382, E344, and G386 from BRD2, BRD3, and BRD4 respectively that mediate cooperative ternary complex formation with VHL are shown in sticks (bottom panel). e Electrostatic surface representation of KLHDC2 highlghting potential basic patches for interaction with BRD3 E344 (left panel). Cartoon representation from ( e ) with relevant basic residues shown in sphere representation (right panel). f Thermodynamic parameters for the indicated ternary complexes between KLHDC2 and the indicated swap mutant BRD proteins and the R56A mutant of KLHDC2. Experiments were performed n = 2 times. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

doi: 10.1038/s41467-024-52966-3

Figure Lengend Snippet: a Thermodynamic parameters for the indicated binary and ternary complexes. Data are the average +/− 1 s.d. from n = 2 experiments. Values for ΔG and ΔH are expressed in kcal/mol −1 . b Biochemical assay monitoring inhibition of KLHDC2 diGly protein substrate ubiquitylation by PROTAC-mediated ternary complex formation, performed as in Fig. . SJ46421-BRD3 BD2 or SJ46421 alone (left panel) or SJ46423-BRD3 BD2 or SJ46423 alone (right panel) were incubated with neddylated CRL2 KLHDC2 , prior to adding fluorescent ubiquitin-charged UBE2R2 (i.e. the pre-formed thioester-linked UBE2R2~ubiquitin intermediate) and diGly protein substrate. Effective PROTAC protein degraders promote ubiquitin transfer to BRD3 BD2 neo-substrate concomitant with loss of diGly substrate ubiquitylation. Samples were reduced when reaction was quenched by addition of SDS buffer. Loss of substrate ubiquitylation was quantified. Shown is representative panels from n = 2 independent experiments. c Quantification of loss of diGly substrate ubiquitylation from the gels in panel. b Data are the average from n = 2 independent experiments. d Sequence alignment of the second bromodomain from BRD2, BRD3, and BRD4. Residue boundaries of the domains are shown, and E344 from BRD3 BD2 is highlighted in red (top panel). Superposition of BRD2 BD2 (salmon; 3ONI.pdb) and BRD3 BD2 (chocolate; 3S92.pdb) to the structure of the VHL-MZL-BRD4 BD2 ternary complex (cyan, orange, and red respectively;5T35.pdb). G382, E344, and G386 from BRD2, BRD3, and BRD4 respectively that mediate cooperative ternary complex formation with VHL are shown in sticks (bottom panel). e Electrostatic surface representation of KLHDC2 highlghting potential basic patches for interaction with BRD3 E344 (left panel). Cartoon representation from ( e ) with relevant basic residues shown in sphere representation (right panel). f Thermodynamic parameters for the indicated ternary complexes between KLHDC2 and the indicated swap mutant BRD proteins and the R56A mutant of KLHDC2. Experiments were performed n = 2 times. Source data are provided as a Source Data file.

Techniques: Inhibition, Ubiquitin Proteomics, Incubation, Sequencing, Residue, Chocolate, Mutagenesis

a Fluorescent scan of gel monitoring SJ46421-dependent BRD3 BD2 ubiquitylation by neddylated versions of CUL2 KLHDC2 , CUL2 KLHDC3 , CUL2 KLHDC10 , or CUL5 KLHDC1 . Assays were performed in pulse-chase format, monitoring PROTAC- and E3-dependent transfer of lysineless (R7) fluorescent ubiquitin from pre-formed thioester-linked UBE2R2~ubiquitin intermediate. Shown is representative panels from n = 2 independent experiments. b Cartoon depiction of the degron-mimic mediated auto-regulation of KLHDC2-EloBC by the inactive tetrameric assembly and active monomer-substrate complexes. c . Fluorescent scan of ubiquitylation assays monitoring the ability of SJ46421-BRD3 BD2 to disrupt the KLHDC2-EloBC tetrameric assembly. Assays were performed as in ( a ). Shown is representative panels from n = 2 independent experiments. d Quantification of the levels ubiquitin conjugated KLHDC2 or BRD3 BD2 form gels in panel ( c ). Data are the average from n = 2 independent experiments. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

doi: 10.1038/s41467-024-52966-3

Figure Lengend Snippet: a Fluorescent scan of gel monitoring SJ46421-dependent BRD3 BD2 ubiquitylation by neddylated versions of CUL2 KLHDC2 , CUL2 KLHDC3 , CUL2 KLHDC10 , or CUL5 KLHDC1 . Assays were performed in pulse-chase format, monitoring PROTAC- and E3-dependent transfer of lysineless (R7) fluorescent ubiquitin from pre-formed thioester-linked UBE2R2~ubiquitin intermediate. Shown is representative panels from n = 2 independent experiments. b Cartoon depiction of the degron-mimic mediated auto-regulation of KLHDC2-EloBC by the inactive tetrameric assembly and active monomer-substrate complexes. c . Fluorescent scan of ubiquitylation assays monitoring the ability of SJ46421-BRD3 BD2 to disrupt the KLHDC2-EloBC tetrameric assembly. Assays were performed as in ( a ). Shown is representative panels from n = 2 independent experiments. d Quantification of the levels ubiquitin conjugated KLHDC2 or BRD3 BD2 form gels in panel ( c ). Data are the average from n = 2 independent experiments. Source data are provided as a Source Data file.

Techniques: Pulse Chase, Ubiquitin Proteomics

a Chemical structure of free-acid and pro-drug PROTAC variants of SJ46421. b Western blot monitoring the levels of the indicated proteins following a 24 h dose of wild-type U2OS or KLHDC2 knockout cells with DMSO, SJ46420, or SJ46421. The asterisk indicates a non-specific reactive band with the KLHDC2 antibody. c Same as ( b ) but with U2OS KLHDC2 KO/rescue cell line and the indicated pro-drug variants. d Same as (c ) but with SJ46420 or SJ48088 in the absence or presence of co-dosing with 1 μM MLN4924. e Volcano plot from TMT proteomics comparing protein levels following a 24 h dose of U2OS KLHDC2 KO/rescue cell line with 1 μM SJ46420. Dashed lines demark proteins stabilized or destabilized > 2-fold with p value < 0.05. Statistical tests used in the volcano plots is two-sided student’s t -test and no correction was made for multiple comparisons. Data are from n = 3 biological replicates. f Same as ( e ) but with U2OS KLHDC2 knockout cells. g Quantification of dose-response western blot monitoring the levels of BRD2, BRD3, and BRD4 following a 24 h dose of U2OS KLHDC2 KO/rescue with the indicated concentration of SJ46420. DC 50 and D max values calculated from the fit shown in the table below are the average from n = 2 independent experiments. h Same as ( g ) but with PC3 cells. i Same as ( g) but with 22Rv1 cells. All data in Fig. b-d are representative panels from n = 2 independent experiments. Source data are provided as a Source Data file.

Journal: Nature Communications

Article Title: Principles of paralog-specific targeted protein degradation engaging the C-degron E3 KLHDC2

doi: 10.1038/s41467-024-52966-3

Figure Lengend Snippet: a Chemical structure of free-acid and pro-drug PROTAC variants of SJ46421. b Western blot monitoring the levels of the indicated proteins following a 24 h dose of wild-type U2OS or KLHDC2 knockout cells with DMSO, SJ46420, or SJ46421. The asterisk indicates a non-specific reactive band with the KLHDC2 antibody. c Same as ( b ) but with U2OS KLHDC2 KO/rescue cell line and the indicated pro-drug variants. d Same as (c ) but with SJ46420 or SJ48088 in the absence or presence of co-dosing with 1 μM MLN4924. e Volcano plot from TMT proteomics comparing protein levels following a 24 h dose of U2OS KLHDC2 KO/rescue cell line with 1 μM SJ46420. Dashed lines demark proteins stabilized or destabilized > 2-fold with p value < 0.05. Statistical tests used in the volcano plots is two-sided student’s t -test and no correction was made for multiple comparisons. Data are from n = 3 biological replicates. f Same as ( e ) but with U2OS KLHDC2 knockout cells. g Quantification of dose-response western blot monitoring the levels of BRD2, BRD3, and BRD4 following a 24 h dose of U2OS KLHDC2 KO/rescue with the indicated concentration of SJ46420. DC 50 and D max values calculated from the fit shown in the table below are the average from n = 2 independent experiments. h Same as ( g ) but with PC3 cells. i Same as ( g) but with 22Rv1 cells. All data in Fig. b-d are representative panels from n = 2 independent experiments. Source data are provided as a Source Data file.

Techniques: Western Blot, Knock-Out, Concentration Assay

BET inhibition blunts HCC cell growth and induces differentiation. (a) Kaplan–Meier overall survival plots stratified by BRD2, BRD3 , and BRD4 mRNA levels from TCGA HCC database. (b) Western blot analysis of indicated proteins from control and BET -knockdown Huh7 cells. (c) Cell number quantification of control and BET -knockdown Huh7 cells after growing for 72 h. (d) Representative clonogenicity assays from replated Huh7 and Hep3B cells after pretreatment with vehicle or JQ-1 (0.5 μmol/L) for 48 h. (e) Colony number quantification of replated Huh7 and Hep3B cells after pretreatment with vehicle or JQ-1 (0.5 μmol/L) for 48 h. (f and g) Representative Huh7 and Hep3B sphere cultures (f) and quantification (g) from the vehicle and JQ-1 pretreatment groups. (h) Huh7 xenograft tumor growth curves from vehicle ( n = 4), JQ-1 ( n = 6), or ABBV075 ( n = 6) pretreatment groups. All statistical graphs except that in a show the mean ± SEM. P values were calculated using a log-rank Mantel–Cox test (a), one-way ANOVA (c and h), and a two-tailed Student’s t -test (e and g). All experiments were performed in biological triplicate. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Journal: Life Metabolism

Article Title: BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer

doi: 10.1093/lifemeta/loae016

Figure Lengend Snippet: BET inhibition blunts HCC cell growth and induces differentiation. (a) Kaplan–Meier overall survival plots stratified by BRD2, BRD3 , and BRD4 mRNA levels from TCGA HCC database. (b) Western blot analysis of indicated proteins from control and BET -knockdown Huh7 cells. (c) Cell number quantification of control and BET -knockdown Huh7 cells after growing for 72 h. (d) Representative clonogenicity assays from replated Huh7 and Hep3B cells after pretreatment with vehicle or JQ-1 (0.5 μmol/L) for 48 h. (e) Colony number quantification of replated Huh7 and Hep3B cells after pretreatment with vehicle or JQ-1 (0.5 μmol/L) for 48 h. (f and g) Representative Huh7 and Hep3B sphere cultures (f) and quantification (g) from the vehicle and JQ-1 pretreatment groups. (h) Huh7 xenograft tumor growth curves from vehicle ( n = 4), JQ-1 ( n = 6), or ABBV075 ( n = 6) pretreatment groups. All statistical graphs except that in a show the mean ± SEM. P values were calculated using a log-rank Mantel–Cox test (a), one-way ANOVA (c and h), and a two-tailed Student’s t -test (e and g). All experiments were performed in biological triplicate. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The following primary antibodies were used: Cell Signaling Technology: phospho-AMPKα (Thr172) (40H9) Rabbit mAb (#2535) and AMPKα (#2532); Abclonal: HSP90 (#A5027), HK2 (#A0994), GLUT1 (#A11208), LDHA (#A0861), GDH1(#A5176), and GLS (#A11043); Proteintech: BRD4 (#67374), MYC (#67447-1-Ig), GOT1 (#14886-1-AP), GOT2 (#14800-1-AP), GPT1 (#16897-1-AP), GPT2 (#16757-1-AP), PSAT1 (#10501-1-AP), and TFAM (#23996-1-AP); Santa Cruz: BRD2 (#sc-514103) and BRD3 (#sc-81202).

Techniques: Inhibition, Western Blot, Control, Knockdown, Two Tailed Test

a , Kaplan–Meier overall survival plots stratified by BRD2, BRD3 and BRD4 mRNA levels from TCGA HCC database. A log-rank Mantel–Cox test was performed between the groups. b , Western blot analysis of indicated proteins from control and BET-knock down Huh7 cells. c Cell number quantification after growing control and BET-knock down Huh7 cells for 72 hours d , Representative clonogenicity assays from replated Huh7 and Hep3B cells after vehicle and JQ-1 (0.5 μM) pretreatment for 48 hours. e , Colony number quantification of replated Huh7 and Hep3B cells after vehicle and JQ-1 (0.5 μM) pretreatment for 48 hours. f, g , Representative Huh7 and Hep3B sphere cultures (h) and quantification (i) from vehicle and JQ-1 pretreatment groups. h , Huh7 xenograft tumor growth curve from vehicle (n=4) and JQ-1 (n=6) or ABBV (n=6) pre-treatment groups. All statistical graphs except ( a ) show the mean ± s.e.m. Except ( a ), P values were calculated using a two-tailed Student’s t-test. All experiments were performed in biological triplicate.

Journal: bioRxiv

Article Title: BET inhibition induces GDH1-dependent glutamine metabolic remodeling and vulnerability in liver cancer

doi: 10.1101/2024.03.20.585859

Figure Lengend Snippet: a , Kaplan–Meier overall survival plots stratified by BRD2, BRD3 and BRD4 mRNA levels from TCGA HCC database. A log-rank Mantel–Cox test was performed between the groups. b , Western blot analysis of indicated proteins from control and BET-knock down Huh7 cells. c Cell number quantification after growing control and BET-knock down Huh7 cells for 72 hours d , Representative clonogenicity assays from replated Huh7 and Hep3B cells after vehicle and JQ-1 (0.5 μM) pretreatment for 48 hours. e , Colony number quantification of replated Huh7 and Hep3B cells after vehicle and JQ-1 (0.5 μM) pretreatment for 48 hours. f, g , Representative Huh7 and Hep3B sphere cultures (h) and quantification (i) from vehicle and JQ-1 pretreatment groups. h , Huh7 xenograft tumor growth curve from vehicle (n=4) and JQ-1 (n=6) or ABBV (n=6) pre-treatment groups. All statistical graphs except ( a ) show the mean ± s.e.m. Except ( a ), P values were calculated using a two-tailed Student’s t-test. All experiments were performed in biological triplicate.

Article Snippet: The following primary antibodies were used: Cell signaling technology: Phospho-AMPKα (Thr172) (40H9) Rabbit mAb (#2535), AMPKα (#2532); Abclonal:HSP90 (#A5027), HK2 (#A0994), GLUT1 (#A11208), LDHA (#A0861), GDH1(#A5176), GLS (#A11043); Proteintech: BRD4 (#67374), MYC (#67447-1-Ig), GOT1 (#14886-1-AP), GOT2 (#14800-1-AP), GPT1 (#16897-1-AP), GPT2(#16757-1-AP), PSAT1(#10501-1-AP), TFAM (#23996-1-AP); Santa Cruz: BRD2 (#sc-514103), BRD3 (#sc-81202).

Techniques: Western Blot, Two Tailed Test

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