SDCBP

Summary

SDCBP (syndecan binding protein, HGNC:10662) is a protein-coding gene on chromosome 8q12.1, encoding Syntenin-1 (O00560). Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis.

The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes.

Source: NCBI Gene 6386 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 40 total
• Druggable target: yes
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
• MANE Select transcript: NM_005625

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10662
Approved symbol	SDCBP
Name	syndecan binding protein
Location	8q12.1
Locus type	gene with protein product
Status	Approved
Aliases	SYCL, MDA-9, SDCBP1
Ensembl gene	ENSG00000137575
Ensembl biotype	protein_coding
OMIM	602217
Entrez	6386

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 34 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000260130, ENST00000413219, ENST00000424270, ENST00000447182, ENST00000447267, ENST00000519115, ENST00000520168, ENST00000520228, ENST00000522243, ENST00000522843, ENST00000523441, ENST00000523483, ENST00000630925, ENST00000870943, ENST00000870944, ENST00000870945, ENST00000870946, ENST00000870947, ENST00000870948, ENST00000870949, ENST00000870950, ENST00000870951, ENST00000870952, ENST00000870953, ENST00000870954, ENST00000870955, ENST00000870956, ENST00000870957, ENST00000870958, ENST00000870959, ENST00000919411, ENST00000919412, ENST00000919413, ENST00000919414, ENST00000919415, ENST00000919416, ENST00000968860, ENST00000968861, ENST00000968862

RefSeq mRNA: 9 — MANE Select: NM_005625 NM_001007067, NM_001007068, NM_001007069, NM_001007070, NM_001330537, NM_001348339, NM_001348340, NM_001348341, NM_005625

CCDS: CCDS47862, CCDS47863, CCDS6172, CCDS83298, CCDS87610

Canonical transcript exons

ENST00000260130 — 9 exons

Exon	Start	End
ENSE00000928402	58578033	58578208
ENSE00000928403	58579623	58579794
ENSE00000928404	58580517	58580608
ENSE00001692000	58553261	58553303
ENSE00002131120	58581686	58582858
ENSE00003497476	58570887	58570965
ENSE00003556973	58575900	58576061
ENSE00003587770	58565019	58565084
ENSE00003592323	58572205	58572314

Expression profiles

Bgee: expression breadth ubiquitous, 304 present calls, max score 99.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 170.9846 / max 4403.5634, expressed in 1822 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
88988	170.9846	1822

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pigmented layer of retina	UBERON:0001782	99.64	gold quality
visceral pleura	UBERON:0002401	99.59	gold quality
amniotic fluid	UBERON:0000173	99.51	gold quality
eye	UBERON:0000970	99.51	gold quality
pleura	UBERON:0000977	99.51	gold quality
palpebral conjunctiva	UBERON:0001812	99.49	gold quality
parietal pleura	UBERON:0002400	99.48	gold quality
germinal epithelium of ovary	UBERON:0001304	99.46	gold quality
blood	UBERON:0000178	99.44	gold quality
skin of hip	UBERON:0001554	99.34	gold quality
ganglionic eminence	UBERON:0004023	99.34	gold quality
monocyte	CL:0000576	99.32	gold quality
mononuclear cell	CL:0000842	99.32	gold quality
ventricular zone	UBERON:0003053	99.31	gold quality
heart right ventricle	UBERON:0002080	99.30	gold quality
leukocyte	CL:0000738	99.29	gold quality
parotid gland	UBERON:0001831	99.25	gold quality
choroid plexus epithelium	UBERON:0003911	99.24	gold quality
lower lobe of lung	UBERON:0008949	99.24	gold quality
cartilage tissue	UBERON:0002418	99.23	gold quality
trabecular bone tissue	UBERON:0002483	99.21	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.18	gold quality
placenta	UBERON:0001987	99.15	gold quality
gall bladder	UBERON:0002110	99.15	gold quality
superficial temporal artery	UBERON:0001614	99.12	gold quality
upper leg skin	UBERON:0004262	99.12	gold quality
esophagus squamous epithelium	UBERON:0006920	99.12	gold quality
pericardium	UBERON:0002407	99.09	gold quality
peritoneum	UBERON:0002358	99.07	gold quality
omental fat pad	UBERON:0010414	99.07	gold quality

Single-cell (SCXA)

Detected in 19 experiment(s), a significant marker in 16.

Experiment	Marker?	Max mean expression
E-HCAD-29	yes	2268.83
E-HCAD-1	yes	78.82
E-MTAB-10287	yes	78.17
E-CURD-122	yes	53.94
E-MTAB-8142	yes	50.97
E-MTAB-8410	yes	46.09
E-HCAD-11	yes	43.89
E-GEOD-134144	yes	43.51
E-CURD-88	yes	29.40
E-MTAB-9221	yes	24.69
E-CURD-112	yes	21.78
E-GEOD-135922	yes	18.65
E-GEOD-93593	yes	12.95
E-MTAB-9801	yes	8.26
E-CURD-46	yes	8.10

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
TP53	Repression

Upstream regulators (CollecTRI, top): AR, CREB3L1

miRNA regulators (miRDB)

101 targeting SDCBP, 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-8485	100.00	77.57	4731
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489

Literature-anchored findings (GeneRIF, showing 40)

• Data show that the functional properties of syntenin are a result of independent interactions with target peptides. (PMID:12679023)
• melanoma metastasis is associated with increased expression of the syntenin gene which may participate in signal transduction and cell adhesion via the multifunctional protein-binding properties of its tandem PDZ domains (PMID:15254681)
• eIF5A may be a regulator of p53, and syntenin might regulate p53 by balancing the regulation of eIF5A signaling to p53 for apoptosis (PMID:15371445)
• This review discusses the identification, structure and function of mda-9/syntenin and delineates future studies to address its role in regulating key physiological and pathological processes. (PMID:15518882)
• Study provides the first direct link between mda-9/syntenin expression and tumor cell dissemination in vivo and indicates that mda-9/syntenin expression activates specific signal transduction pathways. (PMID:16322237)
• Together, these results suggest that downregulation of syntenin by RNA interference could provide a means of inhibiting tumor invasion and possibly metastasis in different cancers, and point to syntenin as a potential cancer biomarker and drug target. (PMID:17451681)
• Syntenin binding to Delta1 plays a dual role in promoting intercellular adhesion and regulating Notch signalling. (PMID:17666427)
• Suggest that syntenin is a physiological suppressor of TRAF6 and plays an inhibitory role in IL-1R- and TLR4- mediated NF-kappaB activation pathways. (PMID:18234474)
• Syntenin stimulates c-jun phosphorylation and modulates Frizzled 7 signaling, in particular the PKCalpha/CDC42 noncanonical Wnt signaling cascade. (PMID:18256285)
• data are compatible with a model wherein interaction of MDA-9/syntenin with c-Src promotes the formation of an active FAK/c-Src signaling complex, leading to enhanced tumor cell invasion and metastatic spread (PMID:18832467)
• Syntenin interacts with the aminoacyl tRNA synthetase complex in a lysyl-tRNA synthetase-dependent manner. (PMID:18839981)
• Data show that syntenin-1 binds to syndecan-1 and participates in the formation of membrane protrusions, and that syntenin-1 recruitment depends on the dephosphorylation of Tyr-309 located within syndecan-1 PDZ binding domain EFYA. (PMID:19228696)
• Syntenin-1 serves as one of IgA-inducing factors for B cells. (PMID:19592421)
• Syntenin forms complexes with multiple IL-5Ralpha chains (PMID:19654410)
• Mda-9/syntenin acts as a molecular adaptor linking PKCalpha and FAK activation in a pathway of FN adhesion by human cancer cells. (PMID:20145126)
• Large/zonula occludens-1 domains of MDA-9 represent a promosing potential therapeutic target for preventing cancer progression and metastatic spread (PMID:20228839)
• ST1 were up-regulated with the malignancy of prostate cancer cell lines and have their potential as serum biomarkers for indicating the developmental stage of prostate cancer. (PMID:20233700)
• showed that overexpression of wild-type MDA-9/syntenin enhances formation of filopodia, whereas MDA-9/syntenin lacking the PDZ domain inhibits the formation of filopodia (PMID:21359963)
• the cytoplasmic domain of syndecan-2 regulates colon cancer cell migration via interaction with syntenin-1. (PMID:21569759)
• mda-9/syntenin, a positive regulator of cancer metastasis, regulates the activation of Akt (also known as protein kinase B) by facilitating ILK adaptor function during adhesion to type I collagen (COL-I) in human breast cancer cells. (PMID:21828040)
• ubiquitin-dependent pathway involving syntenin-1 that is regulated by Ulk1. (PMID:21949238)
• our data demonstrate that the Sox4 C-terminal domain regulates polyubiquitin-independent proteasomal degradation of Sox4 that can be modulated by interaction with syntenin (PMID:21986941)
• MDA-9/syntenin functions as a positive regulator of melanoma progression and metastasis through interactions with c-Src and promotes the formation of an active FAK/c-Src signaling complex leading to NF-k B and matrix metalloproteinase activation. Review. (PMID:22201728)
• mda-9/syntenin is involved in uveal melanoma progression (PMID:22267972)
• the key role of syntenin-1 is the generation of functional asymmetry in T cells and provide a novel mechanistic link between receptor activation and actin polymerization and accumulation in response to extracellular stimulation. (PMID:22349701)
• Data show that syntenin-1 is recruited to the plasma membrane during HIV-1 attachment. (PMID:22535526)
• results indicate Mda-9/syntenin overexpression could activate FAK-JNK and FAK-Akt signaling and then enhance the migration capacity of human brain glioma cells. (PMID:22938480)
• Findings establish RKIP as an inhibitor of MDA-9-dependent melanoma metastasis. (PMID:23066033)
• Our studies delineate an unanticipated cell nonautonomous function of MDA-9/syntenin in the context of angiogenesis, which may directly contribute to its metastasis-promoting properties (PMID:23233738)
• Results suggested that SDCBP played an important role in tumor growth of ER-negative breast cancers. (PMID:23533663)
• Our findings indicate that MDA-9/Syntenin might provide an attractive target for developing detection, monitoring, and therapeutic strategies for managing Urothelial cell carcinoma . (PMID:23873690)
• High MDA-9 expresison is associated with glioma. (PMID:24305713)
• Syntenin-ALIX exosome biogenesis and budding into multivesicular bodies are controlled by ARF6 and PLD2. (PMID:24637612)
• ALCAM stably interacts with actin by binding to syntenin-1 and ezrin. (PMID:24662291)
• MDA-9, co-expressed with GRP78, as a melanoma protein associated with lymph node metastasis. Investigating how MDA-9 and GRP78 interact to contribute to melanoma metastasis and disease progression could reveal new potential avenues of targeted therapy (PMID:25480418)
• these findings demonstrate that syntenin may act as an important positive regulator of TGF-b signaling by regulating caveolin-1-mediated internalization of TbRI; thus, providing a novel function for syntenin that is linked to cancer progression. (PMID:25893292)
• To predict mda-9’s association with extracellular matrix organization. (PMID:26093898)
• Data show that patients with high MDA-9/Syntenin and high Slug expressions were associated with poor overall survival compared to those with low expression in lung adenocarcinomas. (PMID:26561205)
• Data suggest that syntenin/SDCBP PDZ domains 1 and 2 recognize a broad range of peptide ligands with preferences for nectin-1, hydrophobic amino acid motifs, and cryptic internal ligands/peptide fragments. (PMID:26787460)
• Frizzled 7 and phosphatidylinositol 4,5-diphosphate binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signaling. (PMID:27386966)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Sdcbp	ENSMUSG00000028249
rattus_norvegicus	Sdcbp	ENSRNOG00000009683
drosophila_melanogaster	X11Lbeta	FBGN0052677
caenorhabditis_elegans	lin-10	WBGENE00002999

Paralogs (4): APBA3 (ENSG00000011132), APBA2 (ENSG00000034053), APBA1 (ENSG00000107282), SDCBP2 (ENSG00000125775)

Protein

Protein identifiers

Syntenin-1 — O00560 (reviewed: O00560)

Alternative names: Melanoma differentiation-associated protein 9, Pro-TGF-alpha cytoplasmic domain-interacting protein 18, Scaffold protein Pbp1, Syndecan-binding protein 1

All UniProt accessions (4): B4DHN5, E9PBU7, O00560, G5EA09

UniProt curated annotations — full annotation on UniProt →

Function. Multifunctional adapter protein involved in diverse array of functions including trafficking of transmembrane proteins, neuro and immunomodulation, exosome biogenesis, and tumorigenesis. Positively regulates TGFB1-mediated SMAD2/3 activation and TGFB1-induced epithelial-to-mesenchymal transition (EMT) and cell migration in various cell types. May increase TGFB1 signaling by enhancing cell-surface expression of TGFR1 by preventing the interaction between TGFR1 and CAV1 and subsequent CAV1-dependent internalization and degradation of TGFR1. In concert with SDC1/4 and PDCD6IP, regulates exosome biogenesis. Regulates migration, growth, proliferation, and cell cycle progression in a variety of cancer types. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.

Subunit / interactions. Monomer and homodimer. Interacts with SDC1, SDC2, SDC3, SDC4, NRXN2, EPHA7, EPHB1, NF2 isoform 1, TGFA and IL5RA. Interacts with NFASC and PTPRJ. Interacts with SDCBP2. Interacts with PDCD6IP. Forms a complex with PDCD6IP and SDC2. Interacts (via C-terminus) with TGFBR1. Binds to FZD7; this interaction is increased by inositol trisphosphate (IP3). Interacts with SMO.

Subcellular location. Cell junction. Focal adhesion. Adherens junction. Cell membrane. Endoplasmic reticulum membrane. Nucleus. Melanosome. Cytoplasm. Cytosol. Cytoskeleton. Secreted. Extracellular exosome. Membrane raft.

Tissue specificity. Expressed in lung cancers, including adenocarcinoma, squamous cell carcinoma and small-cell carcinoma (at protein level). Widely expressed. Expressed in fetal kidney, liver, lung and brain. In adult highest expression in heart and placenta.

Post-translational modifications. Phosphorylated on tyrosine residues.

Induction. By IFNG/IFN-gamma in melanoma cells.

Isoforms (3)

UniProt ID	Names	Canonical?
O00560-1	1	yes
O00560-2	2
O00560-3	3

RefSeq proteins (9): NP_001007068, NP_001007069, NP_001007070, NP_001007071, NP_001317466, NP_001335268, NP_001335269, NP_001335270, NP_005616* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR036034	PDZ_sf	Homologous_superfamily
IPR051230	APP-Binding	Family

Pfam: PF00595

UniProt features (41 total): strand 14, helix 6, modified residue 3, mutagenesis site 3, short sequence motif 3, splice variant 2, domain 2, binding site 2, initiator methionine 1, chain 1, sequence variant 1, sequence conflict 1, turn 1, region of interest 1

Structure

Experimental structures (PDB)

65 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
1R6J	X-RAY DIFFRACTION	0.73
1NTE	X-RAY DIFFRACTION	1.24
1OBX	X-RAY DIFFRACTION	1.35
9V90	X-RAY DIFFRACTION	1.4
8BLU	X-RAY DIFFRACTION	1.5
8BLV	X-RAY DIFFRACTION	1.5
1W9E	X-RAY DIFFRACTION	1.56
1OBZ	X-RAY DIFFRACTION	1.7
1W9Q	X-RAY DIFFRACTION	1.7
7FT5	X-RAY DIFFRACTION	1.77
7FT9	X-RAY DIFFRACTION	1.77
7FT7	X-RAY DIFFRACTION	1.78
1V1T	X-RAY DIFFRACTION	1.8
7FTD	X-RAY DIFFRACTION	1.8
9VA9	X-RAY DIFFRACTION	1.81
1OBY	X-RAY DIFFRACTION	1.85
7FT6	X-RAY DIFFRACTION	1.85
9VAF	X-RAY DIFFRACTION	1.85
7FSP	X-RAY DIFFRACTION	1.86
9VAI	X-RAY DIFFRACTION	1.86
7FTC	X-RAY DIFFRACTION	1.87
7FSO	X-RAY DIFFRACTION	1.9
9VBB	X-RAY DIFFRACTION	1.9
7FSX	X-RAY DIFFRACTION	1.91
1N99	X-RAY DIFFRACTION	1.94
7FSJ	X-RAY DIFFRACTION	1.97
7FSU	X-RAY DIFFRACTION	1.97
7FST	X-RAY DIFFRACTION	1.98
6R9H	X-RAY DIFFRACTION	2
8HCK	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00560-F1	83.46	0.63

Functional residue map

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

Ligand- & substrate-binding residues (2): 215; 250–251

Post-translational modifications (3): 2, 6, 46

Mutagenesis-validated functional residues (3):

Position	Phenotype
214	disruption of the cooperative binding of c-terminal peptides from fzd7 and phosphatidylinositol-4,5-bisphosphate. impair
215	disruption of the cooperative binding of c-terminal peptides from fzd7 and phosphatidylinositol-4,5-bisphosphate.
250	disruption of the cooperative binding of c-terminal peptides from fzd7 and phosphatidylinositol-4,5-bisphosphate. impair

Function

Pathways and Gene Ontology

Reactome pathways

14 pathways

ID	Pathway
R-HSA-3928664	Ephrin signaling
R-HSA-447043	Neurofascin interactions
R-HSA-5213460	RIPK1-mediated regulated necrosis
R-HSA-5675482	Regulation of necroptotic cell death
R-HSA-6798695	Neutrophil degranulation
R-HSA-1266738	Developmental Biology
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-2682334	EPH-Ephrin signaling
R-HSA-373760	L1CAM interactions
R-HSA-422475	Axon guidance
R-HSA-5218859	Regulated Necrosis
R-HSA-5357801	Programmed Cell Death
R-HSA-9675108	Nervous system development

MSigDB gene sets: 403 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, ACTACCT_MIR196A_MIR196B, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_VESICLE_LOCALIZATION, GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, AAGCCAT_MIR135A_MIR135B, GOBP_GROWTH, GOBP_PROTEIN_TARGETING, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, GOBP_REGULATION_OF_EXOCYTOSIS, IVANOVA_HEMATOPOIESIS_MATURE_CELL

GO Biological Process (18): negative regulation of transcription by RNA polymerase II (GO:0000122), negative regulation of receptor internalization (GO:0002091), protein targeting to membrane (GO:0006612), substrate-dependent cell migration, cell extension (GO:0006930), Ras protein signal transduction (GO:0007265), chemical synaptic transmission (GO:0007268), regulation of mitotic cell cycle (GO:0007346), positive regulation of cell population proliferation (GO:0008284), positive regulation of epithelial to mesenchymal transition (GO:0010718), actin cytoskeleton organization (GO:0030036), positive regulation of cell growth (GO:0030307), positive regulation of cell migration (GO:0030335), positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511), intracellular signal transduction (GO:0035556), positive regulation of phosphorylation (GO:0042327), positive regulation of JNK cascade (GO:0046330), positive regulation of exosomal secretion (GO:1903543), positive regulation of extracellular exosome assembly (GO:1903553)

GO Molecular Function (10): frizzled binding (GO:0005109), interleukin-5 receptor binding (GO:0005137), phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), cytoskeletal adaptor activity (GO:0008093), identical protein binding (GO:0042802), syndecan binding (GO:0045545), protein heterodimerization activity (GO:0046982), protein sequestering activity (GO:0140311), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (23): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), interleukin-5 receptor complex (GO:0005895), adherens junction (GO:0005912), focal adhesion (GO:0005925), membrane (GO:0016020), nuclear membrane (GO:0031965), azurophil granule lumen (GO:0035578), melanosome (GO:0042470), membrane raft (GO:0045121), synapse (GO:0045202), extracellular exosome (GO:0070062), blood microparticle (GO:0072562), extracellular vesicle (GO:1903561), endoplasmic reticulum (GO:0005783), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-10 pathways:

Category	Pathways
Axon guidance	2
EPH-Ephrin signaling	1
L1CAM interactions	1
Regulated Necrosis	1
RIPK1-mediated regulated necrosis	1
Innate Immune System	1
Immune System	1
Nervous system development	1
Programmed Cell Death	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
positive regulation of cellular process	2
intracellular anatomical structure	2
protein binding	2
binding	2
organelle membrane	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
regulation of receptor internalization	1
receptor internalization	1
negative regulation of receptor-mediated endocytosis	1
protein targeting	1
establishment of protein localization to membrane	1
substrate-dependent cell migration	1
plasma membrane bounded cell projection assembly	1
small GTPase-mediated signal transduction	1
anterograde trans-synaptic signaling	1
mitotic cell cycle	1
regulation of cell cycle	1
cell population proliferation	1
regulation of cell population proliferation	1
epithelial to mesenchymal transition	1
regulation of epithelial to mesenchymal transition	1
positive regulation of cell differentiation	1
positive regulation of multicellular organismal process	1
cytoskeleton organization	1
actin filament-based process	1
regulation of cell growth	1
cell growth	1
positive regulation of growth	1
cell migration	1
regulation of cell migration	1
positive regulation of cell motility	1
transforming growth factor beta receptor signaling pathway	1
regulation of transforming growth factor beta receptor signaling pathway	1
positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	1
positive regulation of cellular response to transforming growth factor beta stimulus	1
signal transduction	1
phosphorylation	1

Protein interactions and networks

STRING

2272 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SDCBP	SDC1	P18827	996
SDCBP	CD63	P08962	995
SDCBP	PDCD6IP	Q8WUM4	980
SDCBP	CD9	P21926	896
SDCBP	CADM1	Q9BY67	895
SDCBP	CD81	P18582	888
SDCBP	EGFR	P00533	855
SDCBP	SDC2	P34741	843
SDCBP	TSG101	Q99816	842
SDCBP	CD6	P30203	831
SDCBP	SLC6A5	Q9Y345	830
SDCBP	NRXN2	Q9P2S2	822
SDCBP	IL5RA	Q01344	816
SDCBP	NRXN1	Q9ULB1	815
SDCBP	MMP11	P24347	814

IntAct

1394 interactions, top by confidence:

A	B	Type	Score
SDCBP	RNH1	psi-mi:“MI:0915”(physical association)	0.830
TRAF5	SDCBP	psi-mi:“MI:0915”(physical association)	0.790
SDCBP	KLHL12	psi-mi:“MI:0915”(physical association)	0.790
SDCBP	PNMA1	psi-mi:“MI:0915”(physical association)	0.790
SDCBP	TIFA	psi-mi:“MI:0915”(physical association)	0.790
SDCBP	TRAF5	psi-mi:“MI:0915”(physical association)	0.790
KLHL12	SDCBP	psi-mi:“MI:0915”(physical association)	0.790
SDCBP	NADK	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	HPRT1	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	CRYAA	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	FTL	psi-mi:“MI:0915”(physical association)	0.780
TDO2	SDCBP	psi-mi:“MI:0915”(physical association)	0.780
TRIM32	SDCBP	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	PNMA2	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	HMGB3	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	DMC1	psi-mi:“MI:0915”(physical association)	0.780
FTL	SDCBP	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	TDO2	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	TRIM32	psi-mi:“MI:0915”(physical association)	0.780
SDCBP	CEP55	psi-mi:“MI:0915”(physical association)	0.720
WASL	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
SDCBP	SSNA1	psi-mi:“MI:0915”(physical association)	0.720
HSBP1	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
LDOC1	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
HNRNPC	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
CDA	SDCBP	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (614): SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid), SDCBP (Two-hybrid)

ESM2 similar proteins: A4II46, A6QQZ7, A7MBL8, A8KBF6, B4F7E7, D3ZAA9, E2QY99, O00560, O88910, O88954, P15498, P27870, P29074, P31016, P54100, P70175, P78352, Q08DN7, Q12959, Q13368, Q14168, Q15700, Q16513, Q28C55, Q5PYH6, Q5PYH7, Q5RDQ2, Q5T2T1, Q5U2Y3, Q62108, Q62696, Q62936, Q63622, Q6P0D7, Q6R005, Q8AVG0, Q8BPM2, Q8BVD5, Q8BWW9, Q8N3R9

Diamond homologs: O00560, O08992, P70175, Q09506, Q4KLN0, Q5PYH7, Q5ZM14, Q62936, Q92796, Q99JZ0, Q9H190, Q9JI92, Q9PL97, A0A8P0N4K0, A2RT60, A4D2P6, A8MUH7, D3ZKF5, E1BJW1, E7FDW2, E9Q9W7, F1M386, F1MCA7, F1MSG6, F1PBJ0, O14745, O14907, O61967, O62683, O88951, O88952, O95049, P68907, P70587, P97879, Q0P5F3, Q0QWG9, Q14160, Q15599, Q22638

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
SDCBP	“up-regulates activity”	SOX4	binding
E	“up-regulates activity”	SDCBP	relocalization
SDCBP	“up-regulates activity”	p38

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — HNSC.

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1139 predictions. Top by Δscore:

Variant	Effect	Δscore
8:58553300:C:G	donor_gain	1.0000
8:58565013:CTTTA:C	acceptor_loss	1.0000
8:58565014:TTTA:T	acceptor_loss	1.0000
8:58565015:TTA:T	acceptor_loss	1.0000
8:58565016:TA:T	acceptor_loss	1.0000
8:58565017:A:AG	acceptor_gain	1.0000
8:58565017:A:C	acceptor_loss	1.0000
8:58565018:G:GC	acceptor_gain	1.0000
8:58565018:GA:G	acceptor_gain	1.0000
8:58565018:GAA:G	acceptor_gain	1.0000
8:58565018:GAAGA:G	acceptor_gain	1.0000
8:58567355:G:GT	donor_gain	1.0000
8:58570881:TTTCA:T	acceptor_loss	1.0000
8:58570882:TTCAG:T	acceptor_loss	1.0000
8:58570883:TCAG:T	acceptor_loss	1.0000
8:58570884:CAGGC:C	acceptor_loss	1.0000
8:58570885:A:AG	acceptor_gain	1.0000
8:58570885:A:T	acceptor_loss	1.0000
8:58570885:AG:A	acceptor_gain	1.0000
8:58570886:G:GA	acceptor_gain	1.0000
8:58570886:GG:G	acceptor_gain	1.0000
8:58570886:GGCT:G	acceptor_gain	1.0000
8:58570886:GGCTC:G	acceptor_gain	1.0000
8:58570962:GGAA:G	donor_gain	1.0000
8:58570963:G:T	donor_gain	1.0000
8:58570963:GAA:G	donor_gain	1.0000
8:58570963:GAAG:G	donor_gain	1.0000
8:58570966:G:GG	donor_gain	1.0000
8:58572203:A:AG	acceptor_gain	1.0000
8:58572204:G:GG	acceptor_gain	1.0000

AlphaMissense

1970 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:58576036:G:A	G126E	1.000
8:58578094:G:A	G155E	1.000
8:58575997:G:C	R113P	0.999
8:58576035:G:A	G126R	0.999
8:58576035:G:C	G126R	0.999
8:58576039:T:C	L127P	0.999
8:58578043:T:A	V138D	0.999
8:58578049:T:C	L140P	0.999
8:58578093:G:A	G155R	0.999
8:58578093:G:C	G155R	0.999
8:58578093:G:T	G155W	0.999
8:58578094:G:T	G155V	0.999
8:58578097:A:T	D156V	0.999
8:58578202:G:C	R191P	0.999
8:58578208:G:C	R193T	0.999
8:58578208:G:T	R193M	0.999
8:58579623:G:C	R193S	0.999
8:58579623:G:T	R193S	0.999
8:58579672:G:C	G210R	0.999
8:58579697:T:A	I218K	0.999
8:58579724:C:A	A227E	0.999
8:58579736:G:A	G231D	0.999
8:58579739:T:C	L232P	0.999
8:58576036:G:T	G126V	0.998
8:58578039:T:C	F137L	0.998
8:58578041:T:A	F137L	0.998
8:58578041:T:G	F137L	0.998
8:58578052:T:A	V141D	0.998
8:58578070:C:A	A147D	0.998
8:58578090:T:C	F154L	0.998

dbSNP variants (sampled 300 via entrez): RS1000044173 (8:58566930 C>G), RS1000135383 (8:58553819 G>A), RS1000146784 (8:58561192 A>G), RS1000206805 (8:58573954 GT>G), RS1000213179 (8:58565317 C>T), RS1000436489 (8:58566682 G>GT,GTTTTT), RS1000499286 (8:58567267 G>A), RS1000540767 (8:58567057 A>C), RS1000724830 (8:58553086 G>A,C), RS1000742381 (8:58555389 G>C), RS1000752337 (8:58559716 T>G), RS1000818063 (8:58558013 G>A,T), RS1000865047 (8:58561156 G>A), RS1000942547 (8:58553203 G>A), RS1000976109 (8:58559380 A>G)

Disease associations

OMIM: gene MIM:602217 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST010173_24	Triglyceride levels	3.000000e-20
GCST010204_14	Low density lipoprotein cholesterol levels	2.000000e-56
GCST012046_4	Fasting insulin	1.000000e-06
GCST90002388_245	Lymphocyte count	3.000000e-09
GCST90002393_574	Monocyte count	1.000000e-12
GCST90011899_139	Aspartate aminotransferase levels	1.000000e-11

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004530	triglyceride measurement
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0004587	lymphocyte count
EFO:0005091	monocyte count
EFO:0004736	aspartate aminotransferase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL4739667 (SINGLE PROTEIN), CHEMBL4888448 (PROTEIN COMPLEX)

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

ChEMBL bioactivities

25 potent at pChembl≥5 of 47 total, top 25 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.52	Ki	30	nM	CHEMBL4750927
7.40	Ki	40	nM	CHEMBL4781637
6.77	Ki	170	nM	CHEMBL4799812
6.72	Ki	190	nM	CHEMBL4799812
6.60	Ki	250	nM	CHEMBL4749490
6.60	Ki	250	nM	CHEMBL4758599
6.60	Ki	250	nM	CHEMBL4792861
6.60	Ki	250	nM	CHEMBL4747962
6.40	IC50	400	nM	CHEMBL5439384
6.09	IC50	820	nM	CHEMBL5414896
5.82	IC50	1500	nM	CHEMBL5400712
5.75	Kd	1800	nM	CHEMBL5439384
5.70	Ki	2000	nM	CHEMBL4798461
5.70	Ki	2000	nM	CHEMBL4752622
5.40	IC50	4000	nM	CHEMBL5421218
5.38	IC50	4200	nM	CHEMBL5417771
5.28	IC50	5200	nM	CHEMBL5409717
5.28	IC50	5300	nM	CHEMBL5407115
5.20	IC50	6300	nM	CHEMBL5440871
5.13	IC50	7400	nM	CHEMBL4849179
5.11	IC50	7700	nM	CHEMBL5431937
5.06	IC50	8800	nM	CHEMBL5400307
5.00	Ki	1e+04	nM	CHEMBL4792781
5.00	IC50	1e+04	nM	CHEMBL5434947
5.00	IC50	9900	nM	CHEMBL5412078

PubChem BioAssay actives

25 with measured affinity, of 113 total; 23 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
4-[[(2S)-4-amino-1-[[(2S)-4-amino-1-[[2-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(2S)-1-[[(1S)-2-[[(2S)-3-carboxy-1-[[(1S,2S)-1-carboxy-2-methylbutyl]amino]-1-oxopropan-2-yl]amino]-1-cyclohexyl-2-oxoethyl]amino]-3,3-dimethyl-1-oxobutan-2-yl]amino]-3-(1H-indol-3-yl)-1-oxopropan-2-yl]amino]-3-(1H-imidazol-5-yl)-1-oxopropan-2-yl]amino]-3-hydroxy-1-oxopropan-2-yl]amino]-2-oxoethyl]amino]-1,4-dioxobutan-2-yl]amino]-1,4-dioxobutan-2-yl]carbamoyl]-2-[3-(dimethylamino)-6-dimethylazaniumylidenexanthen-9-yl]benzoate	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.0300	uM
(2S,3S)-2-[[(2S)-2-[[2-[[(2S)-2-[[(2R)-2-[[(2S)-2-[[(2S)-2-[[(2S,3R)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-amino-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3-hydroxybutanoyl]amino]-4-methylpentanoyl]amino]-4-carboxybutanoyl]amino]-3-sulfanylpropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]acetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.0400	uM
(2S,3S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]acetyl]amino]-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3,3-dimethylbutanoyl]amino]-2-cyclohexylacetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708560: Binding affinity to syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) by SPR analysis	ki	0.1700	uM
(2R,3S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-acetamido-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3,3-dimethylbutanoyl]amino]-2-cyclohexylacetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.2500	uM
(2R,3S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R,5S,8R,14R,17S,20R,23S,26R,29S,38S)-38-acetamido-17,20-bis(4-aminobutyl)-2,5,8,14,23,26-hexakis(3-carbamimidamidopropyl)-3,6,9,12,15,18,21,24,27,32,39-undecaoxo-1,4,7,10,13,16,19,22,25,28,33-undecazacyclononatriacontane-29-carbonyl]amino]-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3,3-dimethylbutanoyl]amino]-2-cyclohexylacetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.2500	uM
(2S,3S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2R)-2-[[(2S)-2-[[(2R)-2-[[(2S)-2-[[(2R)-2-[[2-[[(2R)-2-[[(2S)-2-[[(2R)-2-[[(2S)-2-acetamido-6-aminohexanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]acetyl]amino]-5-carbamimidamidopentanoyl]amino]-6-aminohexanoyl]amino]-6-aminohexanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-oxopentanoyl]amino]-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3,3-dimethylbutanoyl]amino]-2-cyclohexylacetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.2500	uM
(2R,3S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[2-[[(2S)-2-acetamido-3-(4-hydroxyphenyl)propanoyl]amino]acetyl]amino]-5-carbamimidamidopentanoyl]amino]-6-aminohexanoyl]amino]-6-aminohexanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-amino-5-oxopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-5-carbamimidamidopentanoyl]amino]-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3,3-dimethylbutanoyl]amino]-2-cyclohexylacetyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	0.2500	uM
(2S)-2-[[(2S)-3-[4-(5-acetyl-2-fluorophenyl)phenyl]-2-(6-bromo-3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	0.4000	uM
(2S)-2-[[(2S)-3-[4-(4-acetamidophenyl)phenyl]-2-(6-bromo-3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	0.8200	uM
(2S)-2-[[(2S)-2-(6-bromo-3-oxo-1H-isoindol-2-yl)-3-[4-[2-fluoro-5-(hydroxymethyl)phenyl]phenyl]propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	1.5000	uM
(4S)-4-[[(2S)-4-amino-2-[[(2S,3R)-2-[[(2S,3R)-2-amino-3-hydroxybutanoyl]amino]-3-hydroxybutanoyl]amino]-4-oxobutanoyl]amino]-5-[[(2S)-1-[[(2S)-1-[[(1S)-1-carboxyethyl]amino]-3-(4-hydroxyphenyl)-1-oxopropan-2-yl]amino]-1-oxo-3-phenylpropan-2-yl]amino]-5-oxopentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	2.0000	uM
(2S,3S)-2-[[(2S)-2-[[(2S,3S)-2-[[(2S,3R)-2-[[(2S)-2-[[(2S)-2-[[(2S)-2-amino-3-hydroxypropanoyl]amino]-3-(1H-imidazol-5-yl)propanoyl]amino]-3-(1H-indol-3-yl)propanoyl]amino]-3-hydroxybutanoyl]amino]-3-methylpentanoyl]amino]-3-carboxypropanoyl]amino]-3-methylpentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	2.0000	uM
(2S)-2-[[(2S)-3-[4-(4-oxochromen-6-yl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	4.0000	uM
(2S)-2-[[(2S)-3-[4-(5-acetyl-2-fluorophenyl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	4.2000	uM
(2S)-2-[[(2S)-2-(6-bromo-3-oxo-1H-isoindol-2-yl)-3-naphthalen-2-ylpropanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	5.2000	uM
(2S)-2-[[(2S)-3-[4-[2-fluoro-5-(hydroxymethyl)phenyl]phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	5.3000	uM
(2S)-2-[[(2S)-3-[4-(2-methyl-3-oxo-1H-isoindol-5-yl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	6.3000	uM
(2S)-3-methyl-2-[3-[4-(4-methylsulfonyloxyphenyl)phenyl]sulfanylpropanoylamino]butanoic acid	1772478: Inhibition of recombinant human full-length GST-tagged syntenin-1/Syndecan-2 complex interaction expressed in Escherichia coli ER2566 measured after 16 hrs by HTRF assay	ic50	7.4000	uM
(2S)-2-[[(2S)-3-[4-(4-acetamidophenyl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	7.7000	uM
(2S)-2-[[(2S)-3-[4-(5-cyano-2-fluorophenyl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	8.8000	uM
(2S)-2-[[(2S)-3-[4-(2-fluorophenyl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	9.9000	uM
(4S)-4-[[2-[[(2S)-6-amino-2-[[(2S)-2-amino-3-hydroxypropanoyl]amino]hexanoyl]amino]acetyl]amino]-5-[[(2S,3R)-1-[[(2S)-1-[[(1S)-1-carboxy-2-methylpropyl]amino]-1-oxopropan-2-yl]amino]-3-hydroxy-1-oxobutan-2-yl]amino]-5-oxopentanoic acid	1708559: Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	ki	10.0000	uM
(2S)-2-[[(2S)-3-[4-(2-fluoro-5-methoxyphenyl)phenyl]-2-(3-oxo-1H-isoindol-2-yl)propanoyl]amino]propanoic acid	2029350: Inhibition of full length N-terminal GST-tagged human syntenin-1 expressed in Escherichia coli ER2566/syndecan2 (unknown origin) interaction incubated for 16 hrs by HTRF assay	ic50	10.0000	uM

CTD chemical–gene interactions

78 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
sodium arsenate	decreases expression, decreases reaction, increases abundance, increases expression	2
arsenite	affects binding, increases reaction, affects expression	2
sodium arsenite	increases abundance, increases expression	2
Air Pollutants	affects cotreatment, decreases expression, increases abundance, affects expression	2
Arsenic	increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, decreases methylation	2
Clozapine	decreases expression, increases expression	2
Ozone	affects cotreatment, decreases expression, increases abundance, affects expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Tretinoin	increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
moringin	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
uranyl acetate	affects expression	1
bisphenol A	increases expression	1
nobiletin	decreases expression, decreases reaction	1
trichostatin A	affects expression	1
beta-lapachone	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
sulforaphane	increases expression	1
coumarin	decreases phosphorylation	1
nivalenol	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1

ChEMBL screening assays

14 unique, capped per target: 14 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4713683	Binding	Inhibition of syntenin-PDZ1-2 domain (unknown origin) expressed in Escherichia coli BL21 (DE3) incubated for 5 mins by fluorescence polarization assay	A High-Affinity Peptide Ligand Targeting Syntenin Inhibits Glioblastoma. — J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TK29	HAP1 SDCBP (-) 1	Cancer cell line	Male
CVCL_XS52	HAP1 SDCBP (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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