BRD9

Summary

BRD9 (bromodomain containing 9, HGNC:25818) is a protein-coding gene on chromosome 5p15.33, encoding Bromodomain-containing protein 9 (Q9H8M2). Plays a role in chromatin remodeling and regulation of transcription.

Enables lysine-acetylated histone binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nucleoplasm. Part of SWI/SNF complex.

Source: NCBI Gene 65980 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 147 total — 1 pathogenic
• Druggable target: yes — 4 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_023924

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25818
Approved symbol	BRD9
Name	bromodomain containing 9
Location	5p15.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13441, SMARCI2
Ensembl gene	ENSG00000028310
Ensembl biotype	protein_coding
OMIM	618465
Entrez	65980

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 13 protein_coding, 9 nonsense_mediated_decay, 5 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000466684, ENST00000467963, ENST00000475706, ENST00000483173, ENST00000483234, ENST00000487688, ENST00000489093, ENST00000489816, ENST00000490814, ENST00000493082, ENST00000494422, ENST00000495265, ENST00000495794, ENST00000497410, ENST00000518250, ENST00000518251, ENST00000519112, ENST00000519838, ENST00000523139, ENST00000869700, ENST00000869701, ENST00000869702, ENST00000869703, ENST00000869704, ENST00000869705, ENST00000869706, ENST00000869707, ENST00000922420, ENST00000944369

RefSeq mRNA: 9 — MANE Select: NM_023924 NM_001009877, NM_001317951, NM_001375861, NM_001375862, NM_001375863, NM_001375877, NM_001375878, NM_001375879, NM_023924

CCDS: CCDS34127, CCDS34128

Canonical transcript exons

ENST00000467963 — 16 exons

Exon	Start	End
ENSE00001894924	863741	864568
ENSE00001936783	892606	892801
ENSE00003504491	891640	891854
ENSE00003506200	883938	884070
ENSE00003522882	871526	871564
ENSE00003539105	891155	891287
ENSE00003558483	881107	881182
ENSE00003561064	887361	887471
ENSE00003611654	889587	889647
ENSE00003619418	879794	879889
ENSE00003621504	876101	876212
ENSE00003630345	878355	878487
ENSE00003649321	889021	889165
ENSE00003654934	865414	865581
ENSE00003680603	886592	886707
ENSE00003692011	870473	870575

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 98.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.5521 / max 170.7506, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
60739	27.5785	1819
60737	0.6744	372
60738	0.2992	113

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	98.54	gold quality
ventricular zone	UBERON:0003053	93.08	gold quality
calcaneal tendon	UBERON:0003701	92.58	gold quality
ganglionic eminence	UBERON:0004023	92.13	gold quality
granulocyte	CL:0000094	92.04	gold quality
thymus	UBERON:0002370	92.01	gold quality
right hemisphere of cerebellum	UBERON:0014890	91.91	gold quality
skin of abdomen	UBERON:0001416	91.74	gold quality
cerebellar hemisphere	UBERON:0002245	91.71	gold quality
cerebellar cortex	UBERON:0002129	91.68	gold quality
skin of leg	UBERON:0001511	91.61	gold quality
left testis	UBERON:0004533	91.58	gold quality
right testis	UBERON:0004534	91.44	gold quality
cortical plate	UBERON:0005343	91.28	gold quality
apex of heart	UBERON:0002098	91.17	gold quality
cerebellum	UBERON:0002037	90.98	gold quality
right uterine tube	UBERON:0001302	90.97	gold quality
mucosa of stomach	UBERON:0001199	90.78	gold quality
left ovary	UBERON:0002119	90.76	gold quality
cardia of stomach	UBERON:0001162	90.74	gold quality
embryo	UBERON:0000922	90.66	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.64	gold quality
right ovary	UBERON:0002118	90.47	gold quality
body of uterus	UBERON:0009853	90.36	gold quality
tongue squamous epithelium	UBERON:0006919	90.31	gold quality
cerebellar vermis	UBERON:0004720	90.29	silver quality
upper lobe of left lung	UBERON:0008952	90.29	gold quality
testis	UBERON:0000473	90.24	gold quality
body of stomach	UBERON:0001161	90.24	gold quality
tibial nerve	UBERON:0001323	90.01	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting BRD9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-3692-5P	99.29	67.04	1421
HSA-MIR-6071	99.16	67.77	1780
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-6868-5P	99.06	65.69	1284
HSA-MIR-140-3P	99.04	67.69	1324
HSA-MIR-628-5P	98.36	67.74	844
HSA-MIR-93-3P	98.15	66.65	1309
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-483-3P	97.77	64.95	731
HSA-MIR-1266-5P	97.71	66.92	1052
HSA-MIR-424-3P	97.20	65.86	385
HSA-MIR-500B-3P	96.49	65.40	1087
HSA-MIR-549A-5P	96.35	68.08	587
HSA-MIR-6823-5P	96.26	65.69	919
HSA-MIR-6767-3P	93.99	66.01	204

Literature-anchored findings (GeneRIF, showing 27)

• The bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 recognize the longer butyryl mark on histones. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks. (PMID:26365797)
• BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma. (PMID:30431433)
• miR-140-3p inhibited squamous cell lung cancer cell proliferation and invasion in vitro and in vivo by targeting BRD9 expression. (PMID:30660651)
• Synergistic inhibition of BDs encoded in BAZ2A/B, BRD9, and BET proteins induces apoptosis of triple-negative breast cancer (TNBC) by a combinatorial suppression of ribosomal DNA transcription and ETS-regulated genes. (PMID:31000582)
• BRD9 is overexpressed in acute myeloid leukemia cells including ex vivo primary blasts compared with CD34(+) cells. By targeting BRD9 expression in AML, we observed an alteration in proliferation and survival, ultimately resulting in the induction of apoptosis. (PMID:31000698)
• Study results demonstrate that mutation of SMARCB1 in malignant rhabdoid tumors (RTs) results in a specific dependence upon a BRD9-SWI/SNF complex that lacks SMARCB1. While BRD9 bromodomain is dispensable, the DUF3512 domain of BRD9 is essential for SWI/SNF integrity survival of SMARCB1-mutant RTs. (PMID:31015438)
• oncogenic roles in human cancers (PMID:31504061)
• High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma. (PMID:32276436)
• The bromodomain containing protein BRD-9 orchestrates RAD51-RAD54 complex formation and regulates homologous recombination-mediated repair. (PMID:32457312)
• BRD9 Is a Critical Regulator of Androgen Receptor Signaling and Prostate Cancer Progression. (PMID:33355184)
• Bromodomain-containing protein 9 promotes hepatocellular carcinoma progression via activating the Wnt/beta-catenin signaling pathway. (PMID:34370992)
• Bromodomain-containing protein 9 is a prognostic biomarker associated with immune infiltrates and promotes tumor malignancy through activating notch signaling pathway in negative HIF-2alpha clear cell renal cell carcinoma. (PMID:34415102)
• Exploring the Value of BRD9 as a Biomarker, Therapeutic Target and Co-Target in Prostate Cancer. (PMID:34944438)
• BRD9 regulates interferon-stimulated genes during macrophage activation via cooperation with BET protein BRD4. (PMID:34983841)
• BRD9 is an essential regulator of glycolysis that creates an epigenetic vulnerability in colon adenocarcinoma. (PMID:35778964)
• BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma. (PMID:35853853)
• The Functional Role and Regulatory Mechanism of Bromodomain-Containing Protein 9 in Human Uterine Leiomyosarcoma. (PMID:35883603)
• Ultra-Rare BRD9 Loss-of-Function Variants Limit the Antiviral Action of Interferon. (PMID:36100643)
• Characterization of the Functional Interplay between the BRD7 and BRD9 Homologues in mSWI/SNF Complexes. (PMID:36484504)
• BRD9 Degradation Disrupts Ribosome Biogenesis in Multiple Myeloma. (PMID:36780189)
• BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma. (PMID:37739089)
• BRD9-mediated control of the TGF-beta/Activin/Nodal pathway regulates self-renewal and differentiation of human embryonic stem cells and progression of cancer cells. (PMID:37870468)
• The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. (PMID:38126767)
• Bromodomain-Containing Protein 9 Regulates Signaling Pathways and Reprograms the Epigenome in Immortalized Human Uterine Fibroid Cells. (PMID:38255982)
• Pan-cancer analyses of bromodomain containing 9 as a novel therapeutic target reveals its diagnostic, prognostic potential and biological mechanism in human tumours. (PMID:38303608)
• BRD9 regulates normal human hematopoietic stem cell function and lineage differentiation. (PMID:38816579)
• TPPP-BRD9 fusion-related gallbladder carcinomas are frequently associated with intracholecystic neoplasia, neuroendocrine carcinoma, and a distinctive small tubular-type adenocarcinoma commonly accompanied with a syringomatous pattern. (PMID:38972607)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	brd9	ENSDARG00000017143
mus_musculus	Brd9	ENSMUSG00000057649
rattus_norvegicus	Brd9	ENSRNOG00000015676
drosophila_melanogaster	Brd7-9	FBGN0031947
caenorhabditis_elegans	swsn-9	WBGENE00007256

Paralogs (2): BRD7 (ENSG00000166164), YBEY (ENSG00000182362)

Protein

Protein identifiers

Bromodomain-containing protein 9 — Q9H8M2 (reviewed: Q9H8M2)

Alternative names: Rhabdomyosarcoma antigen MU-RMS-40.8

All UniProt accessions (7): C9JBY0, Q9H8M2, F2Z2E8, H0YAW8, H0YBF1, H0YBR9, H0YBX9

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in chromatin remodeling and regulation of transcription. Acts as a chromatin reader that recognizes and binds acylated histones: binds histones that are acetylated and/or butyrylated. Component of SWI/SNF chromatin remodeling subcomplex GBAF that carries out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Also orchestrates the RAD51-RAD54 complex formation and thereby plays a role in homologous recombination (HR).

Subunit / interactions. Binds acetylated histones H3 and H4. Binds butyrylated histone H4. Component of the multiprotein chromatin-remodeling subcomplex SWI/SNF called GBAF, which includes at least BICRA or BICRAL (mutually exclusive), BRD9, SS18, the core BAF subunits, SMARCA2/BRM, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, SMARCC1/BAF155, and SMARCD1/BAF60A. Interacts (via N-terminal bromodomain) with acetylated RAD54. Interacts (via C-terminus) with RAD51.

Subcellular location. Nucleus.

Domain organisation. The Bromo domain mediates interaction with histones that have acetylated lysine residues at specific positions. Also recognizes and binds histones that are butyrylated.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (6)

UniProt ID	Names	Canonical?
Q9H8M2-5	1	yes
Q9H8M2-2	2
Q9H8M2-3	3
Q9H8M2-4	4
Q9H8M2-1	5
Q9H8M2-6	6

RefSeq proteins (9): NP_001009877, NP_001304880, NP_001362790, NP_001362791, NP_001362792, NP_001362806, NP_001362807, NP_001362808, NP_076413* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001487	Bromodomain	Domain
IPR021900	DUF3512	Family
IPR036427	Bromodomain-like_sf	Homologous_superfamily
IPR051831	Bromodomain_contain_prot	Family

Pfam: PF00439, PF12024

UniProt features (43 total): compositionally biased region 8, splice variant 7, helix 6, modified residue 4, region of interest 4, sequence variant 4, turn 3, site 2, chain 1, domain 1, cross-link 1, sequence conflict 1, strand 1

Structure

Experimental structures (PDB)

55 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
6BQA	X-RAY DIFFRACTION	1.03
5I40	X-RAY DIFFRACTION	1.04
5I7X	X-RAY DIFFRACTION	1.18
6Y7K	X-RAY DIFFRACTION	1.2
4UIT	X-RAY DIFFRACTION	1.3
6V1B	X-RAY DIFFRACTION	1.35
5JI8	X-RAY DIFFRACTION	1.42
4YY6	X-RAY DIFFRACTION	1.45
5I7Y	X-RAY DIFFRACTION	1.45
4YY4	X-RAY DIFFRACTION	1.47
4YYI	X-RAY DIFFRACTION	1.5
6V0X	X-RAY DIFFRACTION	1.5
6YQW	X-RAY DIFFRACTION	1.5
8AHC	X-RAY DIFFRACTION	1.5
4YYD	X-RAY DIFFRACTION	1.52
5EU1	X-RAY DIFFRACTION	1.6
5IGM	X-RAY DIFFRACTION	1.6
6Y7I	X-RAY DIFFRACTION	1.6
6Y7J	X-RAY DIFFRACTION	1.6
4UIU	X-RAY DIFFRACTION	1.64
5MKY	X-RAY DIFFRACTION	1.67
5F25	X-RAY DIFFRACTION	1.68
6YQS	X-RAY DIFFRACTION	1.68
6YQR	X-RAY DIFFRACTION	1.68
4XY8	X-RAY DIFFRACTION	1.7
5IGN	X-RAY DIFFRACTION	1.7
6V14	X-RAY DIFFRACTION	1.7
4UIV	X-RAY DIFFRACTION	1.72
4NQN	X-RAY DIFFRACTION	1.73
4UIW	X-RAY DIFFRACTION	1.73

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H8M2-F1	63.72	0.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 169 (histone h4k5ac h4k8ac and histone h4k5bu h4k8bu binding); 222 (histone h4k5ac h4k8ac and histone h4k5bu h4k8bu binding)

Post-translational modifications (5): 56, 373, 566, 588, 373

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9933947	Formation of the non-canonical BAF (ncBAF) complex

MSigDB gene sets: 138 (showing top): GCM_GSPT1, IRF1_Q6, GOBP_DNA_DAMAGE_RESPONSE, NIKOLSKY_BREAST_CANCER_5P15_AMPLICON, GOBP_MAINTENANCE_OF_CELL_NUMBER, LIAO_METASTASIS, GOBP_REGULATION_OF_STEM_CELL_POPULATION_MAINTENANCE, TIEN_INTESTINE_PROBIOTICS_24HR_UP, GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GCM_NF2, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS, GOBP_RECOMBINATIONAL_REPAIR, RGAGGAARY_PU1_Q6, GOBP_CHROMATIN_REMODELING, CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS

GO Biological Process (7): double-strand break repair via homologous recombination (GO:0000724), chromatin remodeling (GO:0006338), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of cell population proliferation (GO:0008284), negative regulation of cell differentiation (GO:0045596), positive regulation of stem cell population maintenance (GO:1902459), chromatin organization (GO:0006325)

GO Molecular Function (4): nucleic acid binding (GO:0003676), protein-macromolecule adaptor activity (GO:0030674), histone reader activity (GO:0140566), protein binding (GO:0005515)

GO Cellular Component (6): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), SWI/SNF complex (GO:0016514), site of double-strand break (GO:0035861), GBAF complex (GO:0140288)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
SWI/SNF chromatin remodelers	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	2
SWI/SNF superfamily-type complex	2
recombinational repair	1
double-strand break repair	1
chromatin organization	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
cell differentiation	1
regulation of cell differentiation	1
negative regulation of cellular process	1
negative regulation of developmental process	1
stem cell population maintenance	1
positive regulation of developmental process	1
positive regulation of multicellular organismal process	1
regulation of stem cell population maintenance	1
cellular component organization	1
protein binding	1
molecular adaptor activity	1
nucleosome	1
histone binding	1
chromatin-protein adaptor activity	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
site of DNA damage	1

Protein interactions and networks

STRING

1272 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BRD9	BICRA	Q9NZM4	994
BRD9	BICRAL	Q6AI39	983
BRD9	ARID1A	O14497	956
BRD9	ARID2	Q68CP9	933
BRD9	SMARCC1	Q92922	928
BRD9	ACTL6A	O96019	919
BRD9	SMARCA4	P51532	887
BRD9	SMARCA2	P51531	876
BRD9	PHF10	Q8WUB8	875
BRD9	DPF1	Q92782	865
BRD9	ARID1B	Q8NFD5	856
BRD9	SMARCD1	Q96GM5	828
BRD9	PBRM1	Q86U86	822
BRD9	SMARCE1	Q969G3	816
BRD9	DPF2	Q92785	813

IntAct

53 interactions, top by confidence:

A	B	Type	Score
SMARCB1	ARID1A	psi-mi:“MI:0914”(association)	0.860
SMARCC1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCD1	ARID1A	psi-mi:“MI:0914”(association)	0.790
SMARCC2	ARID1A	psi-mi:“MI:0914”(association)	0.790
SS18	ARID1A	psi-mi:“MI:0914”(association)	0.760
BCL7C	ARID1A	psi-mi:“MI:0914”(association)	0.640
BCL7A	ARID1A	psi-mi:“MI:0914”(association)	0.640
BRD9	CATIP	psi-mi:“MI:0915”(physical association)	0.560
CATIP	BRD9	psi-mi:“MI:0915”(physical association)	0.560
SS18L2	ARID1A	psi-mi:“MI:2364”(proximity)	0.480
SS18L2	ARID1A	psi-mi:“MI:0914”(association)	0.480
GABARAPL1	BRD9	psi-mi:“MI:0407”(direct interaction)	0.440
MAP1LC3B	BRD9	psi-mi:“MI:0407”(direct interaction)	0.440
CXXC4	TIA1	psi-mi:“MI:0914”(association)	0.350
NFE2L1	WDFY3	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (173): CATIP (Two-hybrid), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Synthetic Growth Defect), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-RNA), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS), BRD9 (Affinity Capture-MS)

ESM2 similar proteins: A0JNI5, A2AJT4, A2AQ19, A4IFB1, B1H1X4, D3ZTQ1, O43290, P35269, Q05519, Q12872, Q13435, Q3THK3, Q3UJB0, Q3UQU0, Q3USH5, Q4V7C9, Q53F19, Q568R1, Q5EA53, Q5HZB6, Q5PQQ2, Q5R539, Q5RAD5, Q5XIW8, Q5ZM19, Q66I22, Q6AY96, Q6DDA4, Q6GLZ8, Q6INH5, Q6ZPZ3, Q8BZR9, Q8CFC7, Q8K194, Q8N2M8, Q8N5F7, Q8TF01, Q8VHI6, Q8WVK2, Q923D5

Diamond homologs: A0A286Y9D1, A0A7U2QYM2, A2AUY4, A2BIL7, B2KF05, B2RRD7, B7ZS37, E9Q2Z1, F1R5H6, G5E8P1, G5EF53, O54826, O60885, O74759, O75164, O88379, O88665, O94880, O94953, O95696, P0CB22, P13709, P21675, P25440, P34447, P35817, P51123, P55197, P55198, P55201, Q03330, Q08D75, Q0P4S5, Q10077, Q12311, Q23590, Q29EQ3, Q32S26, Q338B9, Q3UQU0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
BRD9	“form complex”	GBAF	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 45 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of the canonical BAF (cBAF) complex	9	178.4×	1e-17
Formation of the embryonic stem cell BAF (esBAF) complex	9	169.1×	2e-17
Formation of the non-canonical BAF (ncBAF) complex	7	146.9×	4e-13
Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF)	10	142.8×	4e-18
Formation of the polybromo-BAF (pBAF) complex	7	138.8×	6e-13
Regulation of endogenous retroelements	9	103.6×	2e-15
Regulation of MITF-M-dependent genes involved in pigmentation	10	83.0×	6e-16
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	6	56.4×	1e-08

GO biological processes:

GO term	Partners	Fold	FDR
regulation of G0 to G1 transition	9	148.0×	8e-16
regulation of nucleotide-excision repair	9	132.1×	1e-15
nucleosome disassembly	6	117.4×	3e-10
regulation of mitotic metaphase/anaphase transition	9	108.8×	6e-15
positive regulation of double-strand break repair	9	75.5×	2e-13
regulation of G1/S transition of mitotic cell cycle	9	67.3×	4e-13
positive regulation of stem cell population maintenance	8	67.1×	1e-11
positive regulation of T cell differentiation	6	66.7×	1e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

147 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	96
Likely benign	11
Benign	7

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
814656	GRCh37/hg19 5p15.33-15.32(chr5:113576-5194484)x1	Pathogenic

SpliceAI

3730 predictions. Top by Δscore:

Variant	Effect	Δscore
5:865577:CTTCC:C	acceptor_gain	1.0000
5:870466:AACTC:A	donor_loss	1.0000
5:870468:C:A	donor_loss	1.0000
5:870469:TCACC:T	donor_loss	1.0000
5:870470:C:CC	donor_loss	1.0000
5:870471:A:AC	donor_gain	1.0000
5:870471:AC:A	donor_gain	1.0000
5:870472:C:CC	donor_gain	1.0000
5:870472:C:T	donor_loss	1.0000
5:870472:CC:C	donor_gain	1.0000
5:870571:CCAAC:C	acceptor_gain	1.0000
5:870572:CAAC:C	acceptor_gain	1.0000
5:870572:CAACC:C	acceptor_gain	1.0000
5:870573:AAC:A	acceptor_gain	1.0000
5:870574:AC:A	acceptor_gain	1.0000
5:870574:ACC:A	acceptor_loss	1.0000
5:870575:CC:C	acceptor_gain	1.0000
5:870576:C:CA	acceptor_loss	1.0000
5:870576:C:CC	acceptor_gain	1.0000
5:870577:T:A	acceptor_loss	1.0000
5:870585:C:CT	acceptor_gain	1.0000
5:876223:C:CT	acceptor_gain	1.0000
5:878488:C:CC	acceptor_gain	1.0000
5:879789:TTTA:T	donor_loss	1.0000
5:879790:TTACC:T	donor_loss	1.0000
5:879791:TA:T	donor_loss	1.0000
5:879792:A:AG	donor_loss	1.0000
5:884068:CAG:C	acceptor_gain	1.0000
5:884071:C:CC	acceptor_gain	1.0000
5:886639:TTG:T	donor_gain	1.0000

AlphaMissense

3971 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:887380:C:T	G233D	1.000
5:887381:C:G	G233R	1.000
5:887389:A:G	L230P	1.000
5:887401:G:T	A226E	1.000
5:887414:A:C	Y222D	1.000
5:887414:A:G	Y222H	1.000
5:887419:G:A	T220I	1.000
5:887430:A:C	N216K	1.000
5:887430:A:T	N216K	1.000
5:887432:T:C	N216D	1.000
5:887434:T:C	Y215C	1.000
5:887435:A:C	Y215D	1.000
5:887435:A:G	Y215H	1.000
5:887435:A:T	Y215N	1.000
5:887443:G:T	A212E	1.000
5:887445:A:C	N211K	1.000
5:887445:A:T	N211K	1.000
5:887447:T:C	N211D	1.000
5:887451:A:C	C209W	1.000
5:887452:C:T	C209Y	1.000
5:887453:A:G	C209R	1.000
5:887455:A:C	M208R	1.000
5:887455:A:T	M208K	1.000
5:887458:A:G	L207P	1.000
5:889025:A:G	F201S	1.000
5:889097:A:C	I177R	1.000
5:889097:A:T	I177K	1.000
5:889109:T:C	Y173C	1.000
5:889110:A:C	Y173D	1.000
5:889110:A:G	Y173H	1.000

dbSNP variants (sampled 300 via entrez): RS1000099469 (5:892611 T>C), RS1000192567 (5:894648 T>C), RS1000216500 (5:882318 A>G,T), RS1000422709 (5:868584 G>A), RS1000474921 (5:868783 T>C), RS1000697228 (5:891579 G>A,C,T), RS1000722565 (5:873863 C>G), RS1000781769 (5:886678 T>G), RS1000910257 (5:872705 G>A,C), RS1000980254 (5:891504 G>A,C), RS1001020784 (5:867223 G>A), RS1001033934 (5:891293 C>A,T), RS1001114862 (5:877044 C>T), RS1001153323 (5:891750 C>T), RS1001170628 (5:887886 G>A)

Disease associations

OMIM: gene MIM:618465 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002553_8	Pancreatic cancer	1.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (10): CHEMBL3108640 (SINGLE PROTEIN), CHEMBL4879534 (PROTEIN-PROTEIN INTERACTION), CHEMBL5291695 (PROTEIN-PROTEIN INTERACTION), CHEMBL5291941 (SELECTIVITY GROUP), CHEMBL5291943 (SELECTIVITY GROUP), CHEMBL5291944 (SELECTIVITY GROUP), CHEMBL5291945 (SELECTIVITY GROUP), CHEMBL5291946 (SELECTIVITY GROUP), CHEMBL5291965 (PROTEIN-PROTEIN INTERACTION), CHEMBL5465396 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

4 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 81,249 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL535	SUNITINIB	4	79,020
CHEMBL1232461	MOLIBRESIB	2	1,538
CHEMBL4078100	AZD-5153	1	591
CHEMBL4785363	INOBRODIB	1	100

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Bromodomain kinase (BRDK) family

Most potent curated ligand interactions (8 total), top 8:

Ligand	Action	Affinity	Parameter
BI-9564	Inhibition	7.85	pKd
BI-7273	Inhibition	7.72	pIC50
TP-472	Inhibition	7.48	pIC50
I-BRD9	Binding	7.1	pIC50
dBRD9-A	Binding	7.08	pIC50
LP99	Inhibition	7.0	pKd
dBRD9	Binding	6.98	pIC50
compound 50 [PMID: 24313754]	Inhibition	6.5	pIC50

Binding affinities (BindingDB)

72 measured of 466 human assays (466 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
6-[(E)-but-2-enyl]-4-[3-methoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	3 nM	US-10183009: Therapeutic compounds and uses thereof
(E)-1-(4-(6-(but-2-en-1-yl)-2-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-2-chlorobenzoyl)piperidine-4-carboxamide	IC50	3 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-isopropoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	3 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-2-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-4-methoxy-N-(pyrimidin-5-ylmethyl)benzamide	IC50	3 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[2,5-dimethoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	4 nM	US-10183009: Therapeutic compounds and uses thereof
(E)-6-(but-2-en-1-yl)-4-(3-chloro-4-(piperazine-1-carbonyl)phenyl)-2-methyl-1H-pyrrolo[2,3-c]pyridin-7(6H)-one	IC50	4 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-chloro-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	5 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-(cyclopropylmethoxy)-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-	IC50	5 nM	US-10183009: Therapeutic compounds and uses thereof
(E)-4-(4-(3-(3-amino-1H-pyrazol-1-yl)azetidine-1-carbonyl)-3-chlorophenyl)-6-(but-2-en-1-yl)-2-methyl-1H-pyrrolo[2,3-c]pyridin-7(6H)-one	IC50	5 nM	US-10183009: Therapeutic compounds and uses thereof
5-[6-[(E)-but-2-enyl]-2-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-2-(morpholine-4-carbonyl)benzonitrile	IC50	6 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-2-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-4-methoxy-N-(pyrazin-2-ylmethyl)benzamide	IC50	6 nM	US-10183009: Therapeutic compounds and uses thereof
(E)-6-(but-2-en-1-yl)-4-(4-(2-hydroxypropan-2-yl)-2,5-dimethoxyphenyl)-2-methyl-1H-pyrrolo[2,3-c]pyridin-7(6H)-one	IC50	6 nM	US-10183009: Therapeutic compounds and uses thereof
1-[4-[6-[(E)-but-2-enyl]-2-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-2-chloro-benzoyl]piperidine-4-carboxylic acid	IC50	8 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-chloro-4-(4-methylpiperazine-1-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	9 nM	US-10183009: Therapeutic compounds and uses thereof
6-allyl-4-[2,5-dimethoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	9 nM	US-10183009: Therapeutic compounds and uses thereof
4-[4-[3-(3-aminopyrazol-1-yl)azetidine-1-carbonyl]phenyl]-6-[(E)-but-2-enyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	9 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-chloro-4-(pyrrolidine-1-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	10 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-2-methyl-4-[3-methyl-4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	11 nM	US-10183009: Therapeutic compounds and uses thereof
6-allyl-4-[3-chloro-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	12 nM	US-10183009: Therapeutic compounds and uses thereof
6-but-2-enyl-4-[4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	13 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-chloro-4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	13 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-2-methyl-4-[4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	13 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-2-methyl-4-[4-(pyrrolidine-1-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	13 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[4-(1-hydroxy-1-methyl-ethyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	17 nM	US-10183009: Therapeutic compounds and uses thereof
6-butyl-4-[2,5-dimethoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	17 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[4-(1-hydroxy-1-methyl-ethyl)-2-methoxy-phenyl]-1H-pyrrolo[2,3-e]pyridin-7-one	IC50	20 nM	US-10183009: Therapeutic compounds and uses thereof
4-[4-(2-hydroxypropan-2-yl)phenyl]-6-methyl-3aH-pyrrolo[2,3-c]pyridin-7-one	IC50	21 nM	US-10150767: Therapeutic compounds and uses thereof
N-[4-(6-but-2-enyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl)phenyl]methanesulfonamide	IC50	22 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[4-chloro-5-(morpholine-4-carbonyl)-2-pyridyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	22 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-N-[2-(dimethylamino)ethyl]-4-methoxy-benzamide	IC50	23 nM	US-10183009: Therapeutic compounds and uses thereof
N-(2-methoxyethyl)-4-(6-methyl-7-oxo-3aH-pyrrolo[2,3-c]pyridin-4-yl)benzamide	IC50	24 nM	US-10150767: Therapeutic compounds and uses thereof
7-(6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl)-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one	IC50	25 nM	US-10150767: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-4-methoxy-N-propyl-benzamide	IC50	27 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-N-ethyl-4-methoxy-benzamide	IC50	28 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-N-isobutyl-4-methoxy-benzamide	IC50	28 nM	US-10183009: Therapeutic compounds and uses thereof
4-(6-but-2-enyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl)-N-methyl-benzamide	IC50	29 nM	US-10183009: Therapeutic compounds and uses thereof
3-methyl-7-(6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl)-1,3,4,5-tetrahydro-1,5-benzodiazepin-2-one	IC50	31 nM	US-10150767: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[5-chloro-6-(morpholine-4-carbonyl)-3-pyridyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	32 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[2,3-difluoro-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	34 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-4-methoxy-N-methyl-benzamide	IC50	35 nM	US-10183009: Therapeutic compounds and uses thereof
3-[6-[(E)-but-2-enyl]-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-N-(2-hydroxyethyl)-4-methoxy-benzamide	IC50	35 nM	US-10183009: Therapeutic compounds and uses thereof
6-but-2-enyl-4-[3-(pyrrolidine-1-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	39 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[2-methoxy-5-(pyrrolidine-1-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	39 nM	US-10183009: Therapeutic compounds and uses thereof
6-but-2-enyl-4-[3-methoxy-5-(4-methylpiperazine-1-carbonyl)-2-pyridyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	39 nM	US-10183009: Therapeutic compounds and uses thereof
6-butyl-4-(4-(2-hydroxypropan-2-yl)phenyl)-1H-pyrrolo[2,3-c]pyridin-7(6H)-one	IC50	43 nM	US-10183009: Therapeutic compounds and uses thereof
3-(6-butyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl)-4-methoxy-benzonitrile	IC50	46 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-chloro-4-(pyrrolidine-1-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	46 nM	US-10183009: Therapeutic compounds and uses thereof
6-[(E)-but-2-enyl]-4-[3-methoxy-5-(morpholine-4-carbonyl)-2-pyridyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	46 nM	US-10183009: Therapeutic compounds and uses thereof
N,N-dimethyl-3-(6-methyl-7-oxo-3aH-pyrrolo[2,3-c]pyridin-4-yl)benzamide	IC50	53 nM	US-10150767: Therapeutic compounds and uses thereof
6-methyl-4-[4-(1-methylpiperidin-4-yl)phenyl]-2,3,3a,4,5,7a-hexahydro-1H-pyrrolo[2,3-c]pyridin-7-one	IC50	53 nM	US-10150767: Therapeutic compounds and uses thereof

ChEMBL bioactivities

460 potent at pChembl≥5 of 488 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
9.62	Kd	0.24	nM	CHEMBL4861491
9.33	Kd	0.47	nM	CHEMBL4872300
9.12	Kd	0.75	nM	CHEMBL3823478
9.10	Kd	0.7943	nM	CHEMBL3823478
8.75	EC50	1.76	nM	CHEMBL5182441
8.70	Kd	1.995	nM	CHEMBL3769507
8.70	Kd	1.995	nM	CHEMBL4635496
8.70	Ki	1.995	nM	CHEMBL3769507
8.70	Kd	2	nM	CHEMBL5268484
8.70	EC50	2	nM	CHEMBL5182441
8.52	IC50	3	nM	CHEMBL5279182
8.52	IC50	3	nM	CHEMBL5797328
8.52	IC50	3	nM	CHEMBL6001080
8.52	IC50	3	nM	CHEMBL5758923
8.40	EC50	4	nM	CHEMBL5182441
8.40	IC50	4	nM	CHEMBL5268484
8.40	IC50	4	nM	CHEMBL5976371
8.37	Kd	4.3	nM	CHEMBL4776447
8.30	IC50	5	nM	CHEMBL5268484
8.30	Kd	5	nM	CHEMBL5289762
8.30	IC50	5	nM	CHEMBL5591100
8.30	IC50	5	nM	CHEMBL5285110
8.30	IC50	5	nM	CHEMBL6060183
8.30	IC50	5	nM	CHEMBL5897449
8.29	Kd	5.1	nM	CHEMBL5182441
8.23	Kd	5.9	nM	CHEMBL3823101
8.22	IC50	6	nM	CHEMBL5279182
8.22	IC50	6	nM	CHEMBL5268936
8.22	IC50	6	nM	CHEMBL6024983
8.22	IC50	6	nM	CHEMBL5289762
8.20	Kd	6.31	nM	CHEMBL3823101
8.15	IC50	7	nM	CHEMBL5285110
8.14	IC50	7.2	nM	CHEMBL3823478
8.10	IC50	7.943	nM	CHEMBL3770188
8.10	IC50	8	nM	CHEMBL5289762
8.10	IC50	8	nM	CHEMBL5268936
8.10	EC50	8	nM	CHEMBL5182441
8.10	IC50	8	nM	CHEMBL5747853
8.05	IC50	9	nM	CHEMBL3823177
8.05	IC50	9	nM	CHEMBL5280605
8.05	IC50	9	nM	CHEMBL6019408
8.05	IC50	9	nM	CHEMBL5804270
8.05	IC50	9	nM	CHEMBL5876460
8.03	Kd	9.4	nM	CHEMBL3823478
8.00	IC50	10	nM	CHEMBL3769944
8.00	Ki	10	nM	CHEMBL4642341
8.00	EC50	10	nM	CHEMBL5279182
8.00	IC50	10	nM	CHEMBL5883024
7.98	IC50	10.4	nM	CHEMBL3769507
7.96	IC50	11	nM	CHEMBL5280605

PubChem BioAssay actives

295 with measured affinity, of 966 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
5-[4-(2-aminoethyl)anilino]-4-bromo-2-methylpyridazin-3-one	1769028: Binding affinity to BRD9 (unknown origin) by BROMOscan method	kd	0.0002	uM
5-[4-(2-aminoethyl)anilino]-4-chloro-2-methylpyridazin-3-one	1769028: Binding affinity to BRD9 (unknown origin) by BROMOscan method	kd	0.0005	uM
4-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-2-methyl-2,7-naphthyridin-1-one	1309627: Binding affinity to human BRD9 isoform 1 by BROMOScan analysis	kd	0.0008	uM
(2S,4R)-N-[[2-[5-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxo-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]pentoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2S)-2-[(1-fluorocyclopropanecarbonyl)amino]-3,3-dimethylbutanoyl]-4-hydroxypyrrolidine-2-carboxamide	1960449: PROTAC activity at VHL/BRD9 in human Ri-1 cells assessed as degradation of BRD9 protein incubated for 8 hrs by Western blot analysis	ec50	0.0018	uM
6-[(E)-but-2-enyl]-4-[2,5-dimethoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	1958295: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	kd	0.0020	uM
6-[(E)-but-2-enyl]-4-[2,5-dimethoxy-4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1655011: Binding affinity to BRD9 (unknown origin)	kd	0.0020	uM
N’-(1,1-dioxothian-4-yl)-5-ethyl-4-oxo-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide	1279909: Binding affinity to partial length human BRD9 by BROMOscan assay	kd	0.0020	uM
N-[2-methoxy-5-(2-oxa-6-azaspiro[3.3]heptan-6-ylsulfonyl)phenyl]-3-methyl-4-oxo-5,6,7,8-tetrahydro-2H-cyclohepta[c]pyrrole-1-carboxamide	1718525: Binding affinity to human partial length BRD9 (R130 to V259 residues) by bromoKdELECT Discover assay	kd	0.0043	uM
1-methylquinolin-2-one	1929269: Inhibition of BRD9 (unknown origin) by Isothermal titration calorimetry	kd	0.0050	uM
6-[(E)-but-2-enyl]-4-[4-(2-hydroxypropan-2-yl)-2,5-dimethoxyphenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	1958295: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	kd	0.0050	uM
2-(2,6-dioxopiperidin-3-yl)-6-[[3-[4-(2-ethyl-1-oxo-2,7-naphthyridin-4-yl)-2,6-dimethoxybenzoyl]-3-azaspiro[5.5]undecan-9-yl]methyl]-5,7-dihydropyrrolo[3,4-f]isoindole-1,3-dione	2114722: Binding affinity to BRD9 (unknown origin) by TR-FRET assay	ic50	0.0050	uM
4-[4-[(dimethylamino)methyl]-2,5-dimethoxyphenyl]-2-methyl-2,7-naphthyridin-1-one	1309627: Binding affinity to human BRD9 isoform 1 by BROMOScan analysis	kd	0.0059	uM
6-[(E)-but-2-enyl]-4-[3-methoxy-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0060	uM
6-[(E)-but-2-enyl]-4-[3-chloro-4-(morpholine-4-carbonyl)phenyl]-2-methyl-1H-pyrrolo[2,3-c]pyridin-7-one	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0070	uM
7-(3,4-dimethoxyphenyl)-N’-(1,1-dioxothian-4-yl)-5-methyl-4-oxothieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0079	uM
5-[6-[(E)-but-2-enyl]-2-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridin-4-yl]-2-(morpholine-4-carbonyl)benzonitrile	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0080	uM
6-[(E)-but-2-enyl]-2-methyl-4-[3-methyl-4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0090	uM
5-[4-[(3-aminoazetidin-1-yl)methyl]-3,5-dimethoxyphenyl]-1,3-dimethylpyridin-2-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0090	uM
7-[3-(dimethylamino)phenyl]-N’-(1,1-dioxothian-4-yl)-5-methyl-4-oxothieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0100	uM
5-butyl-N’-(1,1-dioxothian-4-yl)-4-oxo-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide	1655018: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	ki	0.0100	uM
6-[(E)-but-2-enyl]-2-methyl-4-[4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0120	uM
N’-(1,1-dioxothian-4-yl)-7-(3-methoxyphenyl)-5-methyl-4-oxothieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0126	uM
7-(3,4-dimethoxyphenyl)-N-(1,1-dioxothian-4-yl)-5-methyl-4-oxothieno[3,2-c]pyridine-2-carboxamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0126	uM
4-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-2-methylisoquinolin-1-one	2191069: Inhibition of amino terminal GST tagged BRD9 (aa 130-259 residues) (unknown origin) expressed in Escherichia coli using biotinylated histone H3 K9/14/18/23Ac (1-28) peptide as substrate incubated for 60 mins by alpha-screen assay	ic50	0.0130	uM
(2S,4R)-1-[(2S)-2-[[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxo-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]acetyl]amino]-3,3-dimethylbutanoyl]-4-hydroxy-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]pyrrolidine-2-carboxamide	1960405: Binding affinity to 6His-tagged human BRD9 bromodomain (134 to 239 residues) expressed in Escherichia coli BL21 (DE3) cells assessed as dissociation constant by ITC analysis	kd	0.0150	uM
N’-(1,1-dioxothian-4-yl)-5-methyl-4-oxo-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0158	uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2179212: Binding affinity against BRD9 (unknown origin) assessed as apparent dissociation constant incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	kd	0.0200	uM
5-[4-[(3-hydroxyazetidin-1-yl)methyl]-3,5-dimethoxyphenyl]-1,3-dimethylpyridin-2-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0210	uM
6-[(E)-but-2-enyl]-4-[4-(morpholine-4-carbonyl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1958295: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	kd	0.0210	uM
6-[(E)-but-2-enyl]-4-[4-(2-hydroxypropan-2-yl)-2-methoxyphenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1958295: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	kd	0.0250	uM
3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide	1655011: Binding affinity to BRD9 (unknown origin)	kd	0.0316	uM
7-[(E)-but-2-enyl]-5-[3-chloro-4-(piperazine-1-carbonyl)phenyl]imidazo[1,5-a]pyrazin-8-one	1639080: Inhibition of BRD9 (unknown origin) using H4 peptide as substrate preincubated for 15 mins followed by substrate addition and measured after 60 mins by Alphascreen assay	ic50	0.0350	uM
8-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-6-methylpyrido[4,3-d]pyrimidin-5-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0370	uM
5-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-1,3,4-trimethylpyridin-2-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0370	uM
7-(3-cyanophenyl)-N’-(1,1-dioxothian-4-yl)-5-methyl-4-oxothieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0398	uM
N’-(1,1-dioxothian-4-yl)-5-methyl-4-oxo-7-phenylthieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0398	uM
2,4-dimethyl-5-[[2-(4-methylpiperazin-1-yl)phenyl]methylamino]pyridazin-3-one	1655018: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	ki	0.0398	uM
4-[(E)-but-2-enyl]-2-methyl-5-[[2-(4-methylpiperazin-1-yl)phenyl]methylamino]pyridazin-3-one	1655018: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	ki	0.0398	uM
8-[[1-(3-amino-2,2-difluoropropanoyl)piperidin-4-yl]amino]-5-(3,6-dihydro-2H-pyran-4-yl)-3-methyl-1H-1,7-naphthyridin-2-one	1766150: Inhibition of human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system measured by BROMOscan assay	ki	0.0398	uM
ethyl N-[6-[3-(methanesulfonamido)-4-methylphenyl]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]carbamate	1995396: Binding affinity to BRD9 (unknown origin) assessed as dissociation constant by site-directed competition binding assay	kd	0.0417	uM
6-[(E)-but-2-enyl]-4-[4-(2-hydroxypropan-2-yl)phenyl]-1H-pyrrolo[2,3-c]pyridin-7-one	1957535: Displacement of biotinylated small-molecule ligand from recombinant His-tagged BRD9 (unknown origin) measured after 10 mins by TR-FRET assay	ic50	0.0530	uM
5-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-1,3-dimethylpyridin-2-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0540	uM
5-[4-[(dimethylamino)methyl]-3,5-dimethoxyphenyl]-1,3,6-trimethylpyridin-2-one	1309640: Inhibition of human N-terminal GST-tagged BRD9 isoform 1 expressed in Escherichia coli using tetra-acetylated histone H4 measured after 60 mins by AlphaScreen assay	ic50	0.0570	uM
4-butyl-2-methyl-5-[[2-(4-methylpiperazin-1-yl)phenyl]methylamino]pyridazin-3-one	1655018: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	ki	0.0631	uM
5-[[2-[4-(3-aminopropyl)piperazin-1-yl]phenyl]methylamino]-2,4-dimethylpyridazin-3-one	1655012: Binding affinity to BRD9 (unknown origin) N-terminal bromodomain by TR-FRET assay	ic50	0.0631	uM
N-(2-methoxy-5-morpholin-4-ylsulfonylphenyl)-3-methyl-4-oxo-5,6,7,8-tetrahydro-2H-cyclohepta[c]pyrrole-1-carboxamide	1718525: Binding affinity to human partial length BRD9 (R130 to V259 residues) by bromoKdELECT Discover assay	kd	0.0670	uM
1-(5-amino-2-chlorophenyl)-3-methyl-5,6,7,8-tetrahydro-2H-cyclohepta[c]pyrrol-4-one	1995396: Binding affinity to BRD9 (unknown origin) assessed as dissociation constant by site-directed competition binding assay	kd	0.0670	uM
N-[2-methoxy-5-(4-methylpiperazin-1-yl)sulfonylphenyl]-3-methyl-4-oxo-5,6,7,8-tetrahydro-2H-cyclohepta[c]pyrrole-1-carboxamide	1718525: Binding affinity to human partial length BRD9 (R130 to V259 residues) by bromoKdELECT Discover assay	kd	0.0680	uM
7-(3,4-dimethoxyphenyl)-N’,5-dimethyl-4-oxothieno[3,2-c]pyridine-2-carboximidamide	1279819: Inhibition of BRD9 (unknown origin) incubated in dark for 30 mins by TR-FRET assay	ic50	0.0794	uM
4-ethyl-2-methyl-5-[[2-(4-methylpiperazin-1-yl)phenyl]methylamino]pyridazin-3-one	1655018: Binding affinity to human partial length BRD9 (R130 to V259 residues) expressed in bacterial expression system by BROMOscan assay	ki	0.0794	uM

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
ginger extract	increases expression, decreases reaction, increases abundance	1
bisphenol A	increases abundance, increases expression, decreases reaction	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression, increases abundance	1
manganese chloride	decreases expression, increases abundance	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
corosolic acid	increases expression	1
abrine	increases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Oils, Volatile	increases abundance, increases expression, decreases reaction	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	increases expression	1

ChEMBL screening assays

363 unique, capped per target: 357 binding, 6 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3111335	Binding	Displacement of H2K9(Ac)K13(Ac)K15(Ac) peptide from BRD9 bromodomain (unknown origin) by AlphaScreen assay	[1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains. — J Med Chem
CHEMBL5210055	Functional	Affinity Phenotypic Cellular interaction (CellTiter-Glo assay (Promega, EOL-1 cell proliferation)) EUB0000004c BRD9	Affinity Phenotypic Cellular Literature for EUbOPEN Chemogenomics Library wave 3

Cellosaurus cell lines

7 cell lines: 6 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B2T1	Abcam HEK293T BRD9 KO	Transformed cell line	Female
CVCL_B7W9	Abcam Raji BRD9 KO	Cancer cell line	Male
CVCL_B9WS	Abcam THP-1 BRD9 KO	Cancer cell line	Male
CVCL_C6YT	Abcam PC-3 BRD9 KO	Cancer cell line	Male
CVCL_D9YU	Ubigene HeLa BRD9 KO	Cancer cell line	Female
CVCL_SF67	HAP1 BRD9 (-) 1	Cancer cell line	Male
CVCL_SF68	HAP1 BRD9 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.