USP5

Summary

USP5 (ubiquitin specific peptidase 5, HGNC:12628) is a protein-coding gene on chromosome 12p13.31, encoding Ubiquitin carboxyl-terminal hydrolase 5 (P45974). Deubiquitinating enzyme that participates in a wide range of cellular processes by specifically cleaving isopeptide bonds between ubiquitin and substrate proteins or ubiquitin itself. It is a common-essential gene (DepMap: required in 98.2% of cancer cell lines).

Ubiquitin (see MIM 191339)-dependent proteolysis is a complex pathway of protein metabolism implicated in such diverse cellular functions as maintenance of chromatin structure, receptor function, and degradation of abnormal proteins. A late step of the process involves disassembly of the polyubiquitin chains on degraded proteins into ubiquitin monomers. USP5 disassembles branched polyubiquitin chains by a sequential exo mechanism, starting at the proximal end of the chain (Wilkinson et al., 1995 [PubMed 7578059]).

Source: NCBI Gene 8078 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 96 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 98.2% of screened cell lines (common-essential)
• MANE Select transcript: NM_001098536

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12628
Approved symbol	USP5
Name	ubiquitin specific peptidase 5
Location	12p13.31
Locus type	gene with protein product
Status	Approved
Aliases	IsoT
Ensembl gene	ENSG00000111667
Ensembl biotype	protein_coding
OMIM	601447
Entrez	8078

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 19 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000229268, ENST00000389231, ENST00000535080, ENST00000537267, ENST00000541969, ENST00000542087, ENST00000542371, ENST00000864801, ENST00000864802, ENST00000864803, ENST00000864805, ENST00000864806, ENST00000864807, ENST00000864808, ENST00000864809, ENST00000864810, ENST00000864811, ENST00000864812, ENST00000933307, ENST00000933308, ENST00000969609, ENST00000969610, ENST00000969611

RefSeq mRNA: 6 — MANE Select: NM_001098536 NM_001098536, NM_001382588, NM_001382589, NM_001382590, NM_001382591, NM_003481

CCDS: CCDS31733, CCDS41743

Canonical transcript exons

ENST00000229268 — 20 exons

Exon	Start	End
ENSE00000716138	6855401	6855526
ENSE00000716140	6855755	6855821
ENSE00000716141	6856017	6856150
ENSE00000716142	6856305	6856450
ENSE00000716143	6856707	6856891
ENSE00000866970	6863186	6863377
ENSE00001164806	6865984	6866632
ENSE00001164815	6852150	6852290
ENSE00003466120	6865164	6865248
ENSE00003507604	6864050	6864195
ENSE00003517798	6859470	6859541
ENSE00003567580	6864722	6864875
ENSE00003592636	6861443	6861617
ENSE00003598137	6860953	6861106
ENSE00003603729	6858424	6858617
ENSE00003607485	6860366	6860491
ENSE00003627363	6857629	6857723
ENSE00003628488	6862470	6862558
ENSE00003654435	6863830	6863973
ENSE00003678539	6860151	6860238

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 95.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 46.7524 / max 206.8603, expressed in 1819 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
123778	46.2988	1819
123777	0.4536	242

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	95.27	gold quality
left testis	UBERON:0004533	95.07	gold quality
right testis	UBERON:0004534	95.04	gold quality
right frontal lobe	UBERON:0002810	95.00	gold quality
right adrenal gland	UBERON:0001233	94.70	gold quality
right adrenal gland cortex	UBERON:0035827	94.48	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.23	gold quality
left adrenal gland	UBERON:0001234	94.13	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.01	silver quality
gastrocnemius	UBERON:0001388	93.97	gold quality
left adrenal gland cortex	UBERON:0035825	93.93	gold quality
stromal cell of endometrium	CL:0002255	93.81	gold quality
cingulate cortex	UBERON:0003027	93.79	gold quality
right coronary artery	UBERON:0001625	93.71	gold quality
adrenal cortex	UBERON:0001235	93.69	gold quality
anterior cingulate cortex	UBERON:0009835	93.69	gold quality
muscle of leg	UBERON:0001383	93.68	gold quality
skin of leg	UBERON:0001511	93.68	gold quality
skin of abdomen	UBERON:0001416	93.37	gold quality
adenohypophysis	UBERON:0002196	93.27	gold quality
apex of heart	UBERON:0002098	93.11	gold quality
adrenal gland	UBERON:0002369	93.07	gold quality
popliteal artery	UBERON:0002250	93.04	gold quality
tibial artery	UBERON:0007610	93.03	gold quality
testis	UBERON:0000473	92.99	gold quality
descending thoracic aorta	UBERON:0002345	92.98	gold quality
ganglionic eminence	UBERON:0004023	92.98	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.94	gold quality
nucleus accumbens	UBERON:0001882	92.87	gold quality
aorta	UBERON:0000947	92.85	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting USP5, 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-6077	99.99	68.04	2299
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4318	99.38	66.94	1505
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-2355-5P	98.83	65.51	1589
HSA-MIR-6501-3P	98.71	67.45	1480
HSA-MIR-7114-5P	98.51	67.87	1349

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.2% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 37)

• Selective upregulation of the ubiquitin-proteasome proteolytic pathway proteins, proteasome zeta chain and isopeptidase T in fetal Down syndrome. (PMID:11771738)
• identification of catalytic site (PMID:12435595)
• We report the crystal structures of the zinc-finger ubiquitin binding domain (ZnF UBP) from the deubiquitinating enzyme isopeptidase T (IsoT, or USP5) alone and in complex with ubiquitin. This domain is required for optimal catalytic activation of IsoT. (PMID:16564012)
• p53 is selectively stabilized because the unanchored polyubiquitin that accumulates after USP5 knockdown is able to compete with ubiquitinated p53 but not with Mdm2 for proteasomal recognition (PMID:19098288)
• Production of the USP5 isoform 2 was strongly correlated with PTBP1 expression in glioblastoma tumor samples and cell lines. (PMID:21976412)
• USP5 uses multiple zinc fluoride (ZnF)-ubiquitin binding protein (UBP) domains for substrate targeting and core catalytic function. (PMID:22283393)
• Local administration of NO may prevent neointimal hyperplasia by inhibiting isopeptidase T levels and activity in the vasculature, thereby inhibiting the 26S proteasome in vascular smooth muscle cells. (PMID:23375434)
• Cellular isopeptidase T deubiquitinating enzyme disassembles free ubiquitin chains to facilitate KSHV K7 degradation. (PMID:23720098)
• polyubiquitin chains by USP5 at sites of damage is important for efficient DSB repair (PMID:24454762)
• A ubiquitin shuttle DC-UbP reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes. (PMID:25207809)
• Used IM-MS analysis to study conformational flexibility of the multidomain deubiquitinating enzyme ubiquitin specific protease 5 (USP5). (PMID:25641936)
• Charge-state distribution and ion mobility analysis revealed that both mono- and tetra-ubiquitin bound to the compact conformation of USP5 only. (PMID:25970461)
• Taken together, our study for the first time clarified that the E3 ligase Smurf1 regulates USP5 protein stability and USP5-mediated TNF-alpha production through the ubiquitin proteasome pathway. (PMID:27133717)
• study demonstrates that USP5 plays a critical role in tumorigenesis and progression of pancreatic cancer by stabilizing FoxM1 protein, and provides a rationale for USP5 being a potential therapeutic approach against pancreatic ductal adenocarcinoma (PMID:28807830)
• USP5 regulates c-Maf stability and multiple myeloma cell survival. (PMID:28933784)
• As unanchored ubiquitin chains are preferred substrates for USP5, authors suggest that USP5 regulates the assembly and disassembly of heat-induced stress granules by mediating the hydrolysis of unanchored ubiquitin chains while USP13 regulates stress granules through deubiquitylating protein-conjugated ubiquitin chains. (PMID:29567855)
• USP5 interacts with and stabilizes SLUG to regulate its abundance through USP5 deubiquitination activities in epithelial-mesenchymal transition of hepatocellular carcinoma. (PMID:30809294)
• Genetic alterations disrupting the TNFAIP3/de-ubiquitinase domain mediate increased susceptibility to systemic lupus erythematosus through the upregulation of PADI4 with resultant protein citrullination and extracellular trap formation. (PMID:31300459)
• Our results revealed that circHECTD1 is a glutaminolysis-associated circRNA that promotes gastric cancer (GC) progression. The circHECTD1/miR-1256/USP5 axis could thus be used as a therapeutic target for GC. (PMID:31371702)
• dysregulation of USP5 SUMOylation after peripheral nerve injury may contribute to the well described alteration in Cav3.2 channel activity (PMID:31455361)
• Ubiquitin specific peptidase 5 promotes ovarian cancer cell proliferation through deubiquitinating HDAC2. (PMID:31727867)
• Ubiquitin specific protease 5 negatively regulates the IFNs-mediated antiviral activity via targeting SMURF1. (PMID:32683298)
• A novel combination therapy targeting ubiquitin-specific protease 5 in MYCN-driven neuroblastoma. (PMID:33658627)
• Ubiquitin-Specific Peptidase 5 is Involved in the Proliferation of Trophoblast Cells by Regulating Wnt/beta-Catenin Signaling. (PMID:33977498)
• USP5 facilitates non-small cell lung cancer progression through stabilization of PD-L1. (PMID:34741014)
• Role of ubiquitin-specific protease 5 in the inflammatory response of chronic periodontitis. (PMID:34953100)
• USP5 promotes breast cancer cell proliferation and metastasis by stabilizing HIF2alpha. (PMID:35102545)
• USP5 enhances SGTA mediated protein quality control. (PMID:35895711)
• Kawasaki disease: ubiquitin-specific protease 5 promotes endothelial inflammation via TNFalpha-mediated signaling. (PMID:36329225)
• A pan-cancer analysis of the role of USP5 in human cancers. (PMID:37268697)
• USP5 promotes lipopolysaccharide-induced apoptosis and inflammatory response by stabilizing the TXNIP protein. (PMID:37534934)
• DEPDC1B-mediated USP5 deubiquitination of beta-catenin promotes breast cancer metastasis by activating the wnt/beta-catenin pathway. (PMID:37642235)
• USP5: Comprehensive insights into structure, function, biological and disease-related implications, and emerging therapeutic opportunities. (PMID:38049041)
• PFKP deubiquitination and stabilization by USP5 activate aerobic glycolysis to promote triple-negative breast cancer progression. (PMID:38217030)
• Ubiquitin-specific protease 5 promotes bladder cancer progression through stabilizing Twist1. (PMID:38218898)
• The deubiquitinase USP5 promotes cholangiocarcinoma progression by stabilizing YBX1. (PMID:38692507)
• USP5 negatively regulates the activation of NLRP3 inflammasomes and participates in the pathological and physiological processes of Sjogren’s syndrome. (PMID:38772301)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	usp5	ENSDARG00000014517
mus_musculus	Usp5	ENSMUSG00000038429
rattus_norvegicus	Usp5	ENSRNOG00000015409

Paralogs (71): USP2 (ENSG00000036672), USP28 (ENSG00000048028), USP36 (ENSG00000055483), USP13 (ENSG00000058056), USP33 (ENSG00000077254), USP40 (ENSG00000085982), USP48 (ENSG00000090686), USP14 (ENSG00000101557), USP11 (ENSG00000102226), USP10 (ENSG00000103194), USP31 (ENSG00000103404), USP42 (ENSG00000106346), USP4 (ENSG00000114316), USP9Y (ENSG00000114374), USP34 (ENSG00000115464), USP35 (ENSG00000118369), USP45 (ENSG00000123552), USP22 (ENSG00000124422), USP9X (ENSG00000124486), USP6 (ENSG00000129204), USP29 (ENSG00000131864), USP26 (ENSG00000134588), USP30 (ENSG00000135093), USP15 (ENSG00000135655), USP37 (ENSG00000135913), USP44 (ENSG00000136014), USP20 (ENSG00000136878), USP8 (ENSG00000138592), USP3 (ENSG00000140455), USP21 (ENSG00000143258), USP43 (ENSG00000154914), USP25 (ENSG00000155313), USP16 (ENSG00000156256), USP24 (ENSG00000162402), USP1 (ENSG00000162607), USP49 (ENSG00000164663), USP38 (ENSG00000170185), USP50 (ENSG00000170236), USP47 (ENSG00000170242), USP32 (ENSG00000170832)

Protein

Protein identifiers

Ubiquitin carboxyl-terminal hydrolase 5 — P45974 (reviewed: P45974)

Alternative names: Deubiquitinating enzyme 5, Isopeptidase T, Ubiquitin thioesterase 5, Ubiquitin-specific-processing protease 5

All UniProt accessions (3): P45974, A0A140VJZ1, F5H571

UniProt curated annotations — full annotation on UniProt →

Function. Deubiquitinating enzyme that participates in a wide range of cellular processes by specifically cleaving isopeptide bonds between ubiquitin and substrate proteins or ubiquitin itself. Affects thereby important cellular signaling pathways such as NF-kappa-B, Wnt/beta-catenin, and cytokine production by regulating ubiquitin-dependent protein degradation. Participates in the activation of the Wnt signaling pathway by promoting FOXM1 deubiquitination and stabilization that induces the recruitment of beta-catenin to Wnt target gene promoter. Regulates the assembly and disassembly of heat-induced stress granules by mediating the hydrolysis of unanchored ubiquitin chains. Promotes lipopolysaccharide-induced apoptosis and inflammatory response by stabilizing the TXNIP protein. Affects T-cell biology by stabilizing the inhibitory receptor on T-cells PDC1. Acts as a negative regulator of autophagy by regulating ULK1 at both protein and mRNA levels. Acts also as a negative regulator of type I interferon production by simultaneously removing both ‘Lys-48’-linked unanchored and ‘Lys-63’-linked anchored polyubiquitin chains on the transcription factor IRF3. Modulates the stability of DNA mismatch repair protein MLH1 and counteracts the effect of the ubiquitin ligase UBR4. Upon activation by insulin, it gets phosphorylated through mTORC1-mediated phosphorylation to enhance YTHDF1 stability by removing ‘Lys-11’-linked polyubiquitination. May also deubiquitinate other substrates such as the calcium channel CACNA1H.

Subunit / interactions. Homodimer. Interacts with TRIML1.

Subcellular location. Cytoplasm. Stress granule. Nucleus.

Post-translational modifications. Ubiquitinated by SMURF1; leading to proteasomal degradation. SUMOylated at Lys-113; SUMOylation affects the interaction with Cav3.2 channels.

Domain organisation. The UBP-type zinc finger domain interacts selectively with an unmodified C-terminus of the proximal ubiquitin. Both UBA domains are involved in polyubiquitin recognition.

Miscellaneous. The UBP-type zinc finger domain crystallizes as a dimer linked by a disulfide bond between the Cys-195 residues of both molecules, but there is no evidence that the full-length USP5 exists as a dimer.

Similarity. Belongs to the peptidase C19 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P45974-1	Long	yes
P45974-2	Short

RefSeq proteins (6): NP_001092006, NP_001369517, NP_001369518, NP_001369519, NP_001369520, NP_003472 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001394	Peptidase_C19_UCH	Domain
IPR001607	Znf_UBP	Domain
IPR009060	UBA-like_sf	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR015940	UBA	Domain
IPR016652	Ubiquitinyl_hydrolase	Family
IPR018200	USP_CS	Conserved_site
IPR028889	USP	Domain
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR041432	UBP13_Znf-UBP_var	Domain
IPR041812	UBP5_UBA1	Domain
IPR050185	Ub_carboxyl-term_hydrolase	Family

Pfam: PF00443, PF00627, PF02148, PF17807

Enzyme classification (BRENDA):

• EC 3.4.19.12 — ubiquitinyl hydrolase 1 (BRENDA: 30 organisms, 328 substrates, 173 inhibitors, 70 Km, 58 kcat entries)

Substrate kinetics (BRENDA)

29 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
UBIQUITIN-7-AMIDO-4-METHYLCOUMARIN	—	7
DABCYL-FKKKGGGDVKE-EDANS	0.0142–0.0616	6
UBIQUITIN 7-AMIDO-4-METHYLCOUMARIN	—	5
UBIQUITIN ETHYL ESTER	0.0006–0.03	5
DABCYL-FRLKGGAPIKGV-EDANS	0.0048–0.0217	3
UBIQUITIN-W-G75A	0.0001–0.0004	2
UBIQUITIN-W-G76A	0.0011–0.002	2
UBIQUITIN-W-H68A	0.0005	2
UBIQUITIN-W-I44A	0.0003–0.0004	2
UBIQUITIN-W-K11A	0.0011–0.0023	2
UBIQUITIN-W-K48A	0.0003–0.0007	2
UBIQUITIN-W-K63A	0.0004–0.0008	2
UBIQUITIN-W-K6A	0.0009–0.0014	2
UBIQUITIN-W-L71A	0.008–0.0198	2
UBIQUITIN-W-L73A	0.0058–0.0104	2

UniProt features (111 total): helix 26, strand 25, turn 15, mutagenesis site 12, binding site 9, modified residue 8, sequence conflict 4, domain 3, active site 2, initiator methionine 1, chain 1, disulfide bond 1, cross-link 1, splice variant 1, zinc finger region 1, region of interest 1

Structure

Experimental structures (PDB)

12 structures.

PDB	Method	Resolution (Å)
7MS7	X-RAY DIFFRACTION	1.45
7MS6	X-RAY DIFFRACTION	1.55
6NFT	X-RAY DIFFRACTION	1.65
6DXT	X-RAY DIFFRACTION	1.95
7MS5	X-RAY DIFFRACTION	1.98
2G45	X-RAY DIFFRACTION	1.99
6DXH	X-RAY DIFFRACTION	2
2G43	X-RAY DIFFRACTION	2.09
6P9G	X-RAY DIFFRACTION	2.1
3IHP	X-RAY DIFFRACTION	2.8
2DAG	SOLUTION NMR
2DAK	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P45974-F1	81.40	0.50

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): 335 (nucleophile); 818 (proton acceptor)

Ligand- & substrate-binding residues (9): 202; 209; 219; 221–224; 232; 259; 261; 264; 199

Post-translational modifications (9): 2, 149, 156, 292, 623, 779, 783, 785, 113

Disulfide bonds (1): 195–816

Mutagenesis-validated functional residues (12):

Position	Phenotype
199	decreased rate of activity and decreased zinc binding.
202	decreased rate of activity.
219	decreased rate of activity.
221–223	loss of polyubiquitin binding and subsequent activation.
221	loss of polyubiquitin hydrolysis. loss of ubiquitin binding; when associated with a-335.
232	decreased rate of activity.
261	loss of polyubiquitin binding.
335	loss of activity. loss of ubiquitin binding; when associated with a-221. lower affinity for triubiquitin and tetraubiqui
335	loss of activity.
435	loss of polyubiquitin binding and hydrolysis.
666	lower affinity for triubiquitin and tetraubiquitin, but no effect on affinity for diubiquitin; when associated with a-33
734	lower affinity for diubiquitin, triubiquitin and tetraubiquitin; when associated with a-335. no effect on activity; when

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-5689880	Ub-specific processing proteases
R-HSA-8866652	Synthesis of active ubiquitin: roles of E1 and E2 enzymes

MSigDB gene sets: 219 (showing top): GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_NEGATIVE_REGULATION_OF_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, CAGCTG_AP4_Q5, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_REGULATION_OF_IMMUNE_RESPONSE, MCAATNNNNNGCG_UNKNOWN

GO Biological Process (15): negative regulation of T cell mediated immune response to tumor cell (GO:0002841), proteolysis (GO:0006508), protein ubiquitination (GO:0016567), protein deubiquitination (GO:0016579), regulation of protein stability (GO:0031647), negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435), positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436), protein K48-linked deubiquitination (GO:0071108), regulation protein catabolic process at presynapse (GO:0140251), negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059), regulation of mitotic cell cycle (GO:0007346), positive regulation of translation (GO:0045727), positive regulation of transcription by RNA polymerase II (GO:0045944), negative regulation of T cell activation (GO:0050868), positive regulation of proteasomal protein catabolic process (GO:1901800)

GO Molecular Function (10): cysteine-type endopeptidase activity (GO:0004197), cysteine-type deubiquitinase activity (GO:0004843), zinc ion binding (GO:0008270), ubiquitin binding (GO:0043130), deubiquitinase activity (GO:0101005), protein binding (GO:0005515), peptidase activity (GO:0008233), cysteine-type peptidase activity (GO:0008234), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), lysosome (GO:0005764), cytosol (GO:0005829), cytoplasmic stress granule (GO:0010494), presynapse (GO:0098793)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Deubiquitination	1
Protein ubiquitination	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
regulation of proteasomal ubiquitin-dependent protein catabolic process	2
proteasome-mediated ubiquitin-dependent protein catabolic process	2
cysteine-type peptidase activity	2
T cell mediated immune response to tumor cell	1
negative regulation of T cell mediated immunity	1
negative regulation of immune response to tumor cell	1
regulation of T cell mediated immune response to tumor cell	1
protein metabolic process	1
protein modification by small protein conjugation	1
cysteine-type deubiquitinase activity	1
protein modification by small protein removal	1
regulation of biological quality	1
negative regulation of proteasomal protein catabolic process	1
negative regulation of ubiquitin-dependent protein catabolic process	1
positive regulation of proteasomal protein catabolic process	1
positive regulation of ubiquitin-dependent protein catabolic process	1
protein deubiquitination	1
presynapse	1
regulation protein catabolic process at synapse	1
ubiquitin-dependent protein catabolic process	1
negative regulation of protein catabolic process	1
regulation of ubiquitin-dependent protein catabolic process	1
mitotic cell cycle	1
regulation of cell cycle	1
translation	1
regulation of translation	1
positive regulation of gene expression	1
positive regulation of protein metabolic process	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
T cell activation	1
regulation of T cell activation	1
negative regulation of lymphocyte activation	1
negative regulation of leukocyte cell-cell adhesion	1
proteasomal protein catabolic process	1
positive regulation of protein catabolic process	1
regulation of proteasomal protein catabolic process	1
endopeptidase activity	1

Protein interactions and networks

STRING

2120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
USP5	UBB	P02248	856
USP5	USP14	P54578	844
USP5	K7ESF6	K7ESF6	819
USP5	ZNF501	Q96CX3	819
USP5	ZNF436	Q9C0F3	819
USP5	ZNF629	Q9UEG4	819
USP5	ZNF44	P15621	818
USP5	ZNF569	Q5MCW4	818
USP5	USP7	Q93009	787
USP5	ZUP1	Q96AP4	775
USP5	UCHL3	P15374	769
USP5	UCHL5	Q9Y5K5	768
USP5	CACNA1H	O95180	763
USP5	USP39	Q53GS9	755
USP5	STUB1	Q9UNE7	746

IntAct

66 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
USP5	DAZAP2	psi-mi:“MI:0915”(physical association)	0.560
USP5	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
DAZAP2	USP5	psi-mi:“MI:0915”(physical association)	0.560
TMEM239	USP5	psi-mi:“MI:0915”(physical association)	0.560
TMEM31	PSMD11	psi-mi:“MI:0914”(association)	0.530
TCEAL1	CHEK1	psi-mi:“MI:0914”(association)	0.530
TADA3	USP5	psi-mi:“MI:0915”(physical association)	0.510
	USP5	psi-mi:“MI:0407”(direct interaction)	0.440
USP5	UBC	psi-mi:“MI:0204”(deubiquitination reaction)	0.440
USP13	USP5	psi-mi:“MI:0915”(physical association)	0.400
USP5	RAD23B	psi-mi:“MI:0915”(physical association)	0.400
RAD23B	USP5	psi-mi:“MI:0915”(physical association)	0.400
USP5	ENTREP1	psi-mi:“MI:0915”(physical association)	0.370
USP5	RNF11	psi-mi:“MI:0915”(physical association)	0.370
DVL2	USP5	psi-mi:“MI:0915”(physical association)	0.370
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
BCL2L14		psi-mi:“MI:0914”(association)	0.350
	RNH1	psi-mi:“MI:0914”(association)	0.350
CAV1	ACOT7	psi-mi:“MI:0914”(association)	0.350
rep	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (348): USP5 (Affinity Capture-MS), USP5 (Affinity Capture-Western), USP5 (Co-crystal Structure), USP5 (Reconstituted Complex), UBA1 (Affinity Capture-Western), UBTD2 (Affinity Capture-Western), PLA2G2A (Biochemical Activity), UBC (Reconstituted Complex), UBC (Co-crystal Structure), DAZAP2 (Two-hybrid), TMEM239 (Two-hybrid), USP5 (Affinity Capture-RNA), USP5 (Affinity Capture-RNA), USP5 (Reconstituted Complex), UBC (Reconstituted Complex)

ESM2 similar proteins: A0A0R4IB93, A1CEK7, A1DFN6, A1Z7K9, A2QW83, A4RF51, E1BMF7, E1BY77, F1QFS9, F6V6I0, G0SAK8, O48534, P0C581, P38237, P40826, P43593, P45974, P54201, P54578, P56399, P60051, Q09879, Q0CJU7, Q0IIF7, Q0UPL5, Q11119, Q17361, Q1E873, Q2GSV2, Q2ULU6, Q3V0C5, Q4VSI4, Q4WHP6, Q5BBL5, Q5BKP2, Q5R407, Q5ZM45, Q6A4J8, Q6U7I1, Q76LT8

Diamond homologs: A6QR55, A6ZY34, A7TGY3, A7Z056, B2GUX4, B2GUZ1, B3LGK1, D6RBM5, E9Q9U0, E9QG68, F6Z5C0, F8VPZ3, G5E8G2, G5E8I7, M9PD06, O22207, O57429, O60079, O75604, O88623, O94966, P32571, P35123, P35125, P39538, P39944, P40818, P40826, P45974, P51784, P54578, P56399, P60051, Q01988, Q0E2F9, Q0IIF7, Q13107, Q2HJE4, Q2KHV7, Q2KJ72

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
USP5	“up-regulates quantity”	UBB	cleavage
USP5	“up-regulates quantity”	UBC	cleavage
USP5	“up-regulates quantity”	Ubiquitin	cleavage
USP5	“up-regulates quantity by stabilization”	FOXM1	deubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	71
Likely benign	2
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

2913 predictions. Top by Δscore:

Variant	Effect	Δscore
12:6852287:GCCG:G	donor_gain	1.0000
12:6852290:GGT:G	donor_loss	1.0000
12:6852291:G:GG	donor_gain	1.0000
12:6852291:GTAAG:G	donor_loss	1.0000
12:6855398:CAG:C	acceptor_loss	1.0000
12:6855399:A:AG	acceptor_gain	1.0000
12:6855400:G:GA	acceptor_loss	1.0000
12:6855400:G:GG	acceptor_gain	1.0000
12:6855400:GGA:G	acceptor_gain	1.0000
12:6855522:GCCCG:G	donor_gain	1.0000
12:6855524:CCGG:C	donor_loss	1.0000
12:6855525:CG:C	donor_loss	1.0000
12:6855526:GG:G	donor_loss	1.0000
12:6855527:G:GG	donor_gain	1.0000
12:6855527:GTAG:G	donor_loss	1.0000
12:6855528:T:G	donor_loss	1.0000
12:6855751:ACAG:A	acceptor_loss	1.0000
12:6855752:CAGA:C	acceptor_loss	1.0000
12:6855753:A:AG	acceptor_gain	1.0000
12:6855754:G:GA	acceptor_gain	1.0000
12:6855754:GAA:G	acceptor_gain	1.0000
12:6855754:GAAA:G	acceptor_gain	1.0000
12:6855818:ATTGG:A	donor_loss	1.0000
12:6855822:G:GG	donor_gain	1.0000
12:6855822:GTGAG:G	donor_loss	1.0000
12:6855823:T:G	donor_loss	1.0000
12:6856007:A:AG	acceptor_gain	1.0000
12:6856008:T:G	acceptor_gain	1.0000
12:6856015:A:AG	acceptor_gain	1.0000
12:6856015:AG:A	acceptor_gain	1.0000

AlphaMissense

5646 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:6852253:T:A	V25D	1.000
12:6852267:T:C	C30R	1.000
12:6856371:T:A	W169R	1.000
12:6856371:T:C	W169R	1.000
12:6856373:G:C	W169C	1.000
12:6856373:G:T	W169C	1.000
12:6856717:T:C	C199R	1.000
12:6856747:T:A	W209R	1.000
12:6856747:T:C	W209R	1.000
12:6856749:G:C	W209C	1.000
12:6856749:G:T	W209C	1.000
12:6856751:T:C	L210P	1.000
12:6856777:T:C	C219R	1.000
12:6856778:G:A	C219Y	1.000
12:6856779:T:G	C219W	1.000
12:6856781:G:A	G220E	1.000
12:6856859:T:A	V246D	1.000
12:6856861:A:G	K247E	1.000
12:6856863:G:C	K247N	1.000
12:6856863:G:T	K247N	1.000
12:6856874:T:A	I251N	1.000
12:6857637:T:C	S260P	1.000
12:6857686:T:C	L276P	1.000
12:6858478:T:A	W307R	1.000
12:6858478:T:C	W307R	1.000
12:6858480:G:C	W307C	1.000
12:6858480:G:T	W307C	1.000
12:6858562:T:C	C335R	1.000
12:6858563:G:A	C335Y	1.000
12:6858564:C:G	C335W	1.000

dbSNP variants (sampled 300 via entrez): RS1000125271 (12:6859545 T>C,G), RS1000165675 (12:6865564 G>C), RS1000300966 (12:6865861 G>A,C), RS1001038290 (12:6864505 C>G,T), RS1001404924 (12:6853305 G>A,C), RS1001642322 (12:6859780 G>A), RS1001731071 (12:6866639 C>T), RS1002009462 (12:6860008 T>C), RS1002068109 (12:6865007 G>A), RS1002375947 (12:6858581 T>A,C), RS1002607503 (12:6861703 T>A), RS1003048231 (12:6861319 A>G,T), RS1003745043 (12:6854764 A>C,G,T), RS1003798740 (12:6855146 G>A), RS1003943370 (12:6855773 A>G)

Disease associations

OMIM: gene MIM:601447 | 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
GCST010002_206	Refractive error	3.000000e-62

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6158 (SINGLE PROTEIN)

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

PharmGKB variants

4 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs5442	CDCA3, GNB3, USP5		0.00	0
rs5443	CDCA3, GNB3, USP5	3	5.00	15	bumetanide;furosemide;torasemide;methadone;atenolol;antidepressants;HMG-CoA reductase inhibitors;sumatriptan;olanzapine;sildenafil;nortriptyline;Beta Blocking Agents
rs2301339	CDCA3, GNB3, USP5	3	9.25	1	atenolol
rs12302749	TPI1, USP5	3	0.00	1	methylphenidate

GtoPdb / IUPHAR curated pharmacology

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

Target class: enzyme — C19: Ubiquitin-specific protease

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
vialinin A	Inhibition	5.4	pKi

ChEMBL bioactivities

20 potent at pChembl≥5 of 67 total, top 20 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.01	Kd	9.876	nM	CHEMBL5653589
8.01	ED50	9.876	nM	CHEMBL5653589
6.10	IC50	800	nM	CHEMBL5278336
5.55	Kd	2800	nM	CHEMBL5278336
5.52	IC50	3000	nM	CHEMBL1923233
5.51	Kd	3100	nM	CHEMBL5266862
5.47	Kd	3400	nM	CHEMBL5266862
5.40	Ki	4000	nM	VIALININ A
5.35	Kd	4500	nM	CHEMBL5410606
5.23	IC50	5900	nM	VIALININ A
5.20	Kd	6300	nM	CHEMBL5426708
5.16	Kd	7000	nM	CHEMBL5270943
5.16	Kd	7000	nM	CHEMBL5267510
5.16	IC50	7000	nM	CHEMBL5278336
5.10	Kd	8000	nM	CHEMBL5273203
5.10	Kd	8000	nM	CHEMBL5278336
5.10	IC50	8000	nM	CHEMBL5410606
5.07	EC50	8600	nM	CHEMBL4303622
5.05	Kd	9000	nM	CHEMBL5267112
5.05	Kd	9000	nM	CHEMBL5271929

PubChem BioAssay actives

19 with measured affinity, of 157 total; 13 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-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149746: Binding affinity to human USP5 incubated for 45 mins by Kinobead based pull down assay	kd	0.0099	uM
2-[[5-[4-(4-chlorophenyl)piperidin-1-yl]sulfonylpyridine-2-carbonyl]amino]acetic acid	1925850: Inhibition of full length USP5 (1 to 835 residues) (unknown origin) expressed in Escherichia coli using DU48-03 as substrate preincubated with enzyme for 1 hr followed by substrate addition and measured for 10 mins by IQF assay	ic50	0.8000	uM
(E)-3-(6-bromo-2-pyridinyl)-2-cyano-N-[(1S)-1-phenylbutyl]prop-2-enamide	761493: Inhibition of USP5 in human Z138 cells after 1 hr by immunoblotting analysis	ic50	3.0000	uM
potassium 2-[[5-[4-(4-chlorophenyl)piperidin-1-yl]sulfonylpyridine-2-carbonyl]amino]acetate	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	3.1000	uM
[3,4-dihydroxy-2,5-bis(4-hydroxyphenyl)-6-(2-phenylacetyl)oxyphenyl] 2-phenylacetate	761509: Inhibition of wild type human USP5 expressed in Escherichia coli BL21(DE3) using Ub-AMC as substrate after 60 mins by fluorometric analysis	ki	4.0000	uM
3-[8-chloro-3-[2-[(2-methoxyphenyl)methylamino]-2-oxoethyl]-4-oxoquinazolin-2-yl]propanoic acid	2010540: Binding affinity to N-terminal Avi-tagged and C-terminal His6-tagged USP5 (171 to 290 residues) (unknown origin) expressed in Escherichia coli BirA assessed as dissociation constant by SPR analysis	kd	4.5000	uM
3-[8-chloro-3-[2-[(2-methoxyphenyl)methyl-methylamino]-2-oxoethyl]-4-oxoquinazolin-2-yl]propanoic acid	2010540: Binding affinity to N-terminal Avi-tagged and C-terminal His6-tagged USP5 (171 to 290 residues) (unknown origin) expressed in Escherichia coli BirA assessed as dissociation constant by SPR analysis	kd	6.3000	uM
2-[[5-(4-phenylpiperidin-1-yl)sulfonylpyridine-2-carbonyl]amino]acetic acid	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	7.0000	uM
2-[[4-[4-(4-chlorophenyl)piperidin-1-yl]sulfonyl-2-fluorobenzoyl]amino]acetic acid	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	7.0000	uM
4-oxo-4-[4-(4-phenylpiperidin-1-yl)sulfonylphenyl]butanoic acid	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	8.0000	uM
(2,6-diamino-5-thiocyanato-3-pyridinyl) thiocyanate	1925873: Inhibition of USP5 (unknown origin)	ec50	8.6000	uM
4-oxo-4-[4-(4-pyrrolidin-1-ylpiperidin-1-yl)sulfonylphenyl]butanoic acid	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	9.0000	uM
2-[[2-fluoro-4-(4-phenylpiperidin-1-yl)sulfonylbenzoyl]amino]acetic acid	1925840: Binding affinity to biotinylated USP5 zinc finger ubiquitin binding domain (171 to 290 residues) (unknown origin) expressed in Escherichia coli by surface plasmon resonance assay	kd	9.0000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, increases expression	3
Air Pollutants	increases abundance, decreases expression, affects expression	2
Cadmium	decreases reaction, increases abundance, increases palmitoylation, increases expression	2
Smoke	decreases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Cadmium Chloride	decreases reaction, increases abundance, increases palmitoylation, increases expression	2
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	increases expression	1
bisphenol A	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression, increases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
ochratoxin A	increases expression	1
epigallocatechin gallate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
abrine	decreases expression	1
quinocetone	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Arsenic	affects methylation	1

ChEMBL screening assays

61 unique, capped per target: 61 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1243705	Binding	Inhibition of isopeptidase T	Mechanisms, biology and inhibitors of deubiquitinating enzymes. — Nat Chem Biol

Cellosaurus cell lines

1 cell lines: 1 telomerase immortalized cell line

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

Cellosaurus	Name	Category	Sex
CVCL_C3KY	N/Tert-1 USP5	Telomerase immortalized cell line	Male

Clinical trials (associated diseases)

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