UBLCP1

Summary

UBLCP1 (ubiquitin like domain containing CTD phosphatase 1, HGNC:28110) is a protein-coding gene on chromosome 5q33.3, encoding Ubiquitin-like domain-containing CTD phosphatase 1 (Q8WVY7). Dephosphorylates 26S nuclear proteasomes, thereby decreasing their proteolytic activity.

Enables proteasome regulatory particle binding activity and protein serine/threonine phosphatase activity. Involved in negative regulation of ATP-dependent activity and regulation of proteasome assembly. Located in nucleolus and nucleoplasm.

Source: NCBI Gene 134510 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 41 total
• Druggable target: yes
• MANE Select transcript: NM_145049

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28110
Approved symbol	UBLCP1
Name	ubiquitin like domain containing CTD phosphatase 1
Location	5q33.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC10067, CPUB1
Ensembl gene	ENSG00000164332
Ensembl biotype	protein_coding
OMIM	609867
Entrez	134510

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 retained_intron

ENST00000296786, ENST00000519276, ENST00000521738, ENST00000874190, ENST00000874191, ENST00000874192, ENST00000874193, ENST00000923627

RefSeq mRNA: 1 — MANE Select: NM_145049 NM_145049

CCDS: CCDS4345

Canonical transcript exons

ENST00000296786 — 11 exons

Exon	Start	End
ENSE00001083621	159272023	159272121
ENSE00001083626	159263290	159263360
ENSE00001083627	159270528	159270643
ENSE00001083628	159269908	159269999
ENSE00001083629	159270360	159270445
ENSE00001083630	159274585	159274622
ENSE00001083634	159268870	159269069
ENSE00003510134	159283212	159283339
ENSE00003617081	159278238	159278354
ENSE00003639433	159284904	159286036
ENSE00003660807	159275148	159275246

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 96.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 42.3680 / max 1661.9847, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59869	42.3680	1815

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	96.67	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.21	gold quality
oviduct epithelium	UBERON:0004804	95.68	gold quality
pons	UBERON:0000988	94.53	gold quality
lower lobe of lung	UBERON:0008949	93.70	gold quality
ileal mucosa	UBERON:0000331	93.66	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.51	gold quality
penis	UBERON:0000989	93.37	gold quality
buccal mucosa cell	CL:0002336	92.92	gold quality
ventral tegmental area	UBERON:0002691	92.76	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.71	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.71	gold quality
superior vestibular nucleus	UBERON:0007227	92.31	gold quality
prefrontal cortex	UBERON:0000451	92.26	gold quality
medulla oblongata	UBERON:0001896	92.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.99	gold quality
lymph node	UBERON:0000029	91.97	gold quality
smooth muscle tissue	UBERON:0001135	91.93	gold quality
lateral nuclear group of thalamus	UBERON:0002736	91.88	gold quality
dorsal root ganglion	UBERON:0000044	91.72	gold quality
cortical plate	UBERON:0005343	91.72	gold quality
inferior vagus X ganglion	UBERON:0005363	91.69	gold quality
layer of synovial tissue	UBERON:0007616	91.59	gold quality
parietal lobe	UBERON:0001872	91.44	gold quality
skin of hip	UBERON:0001554	91.42	gold quality
nasal cavity mucosa	UBERON:0001826	91.40	gold quality
substantia nigra pars compacta	UBERON:0001965	91.39	gold quality
superior surface of tongue	UBERON:0007371	91.39	gold quality
vermiform appendix	UBERON:0001154	91.36	gold quality
entorhinal cortex	UBERON:0002728	91.23	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.15
E-MTAB-6075	no	306.62
E-GEOD-99795	no	115.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

82 targeting UBLCP1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4420	99.82	70.08	1624

Literature-anchored findings (GeneRIF, showing 5)

• UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity (PMID:21949367)
• the high-resolution solution structure of the UBL domain of human UBLCP1 and its interaction with Rpn1 (PMID:23667555)
• Data show that UBLCP1 selectively binds to the 26S proteasome non-ATPase regulatory subunit 13 (19S regulatory particle) in regulating proteasome assembly. (PMID:28539385)
• Study provides evidence that Rpn1-Ser361 is a prevalent phosphosite that is required for proper assembly and activity of the 26S proteasome and identified multiple kinases, including PIM1/2/3, that can phosphorylate Rpn1-S361 and have demonstrated that UBLCP1 is a physiologically relevant phosphatase of this site. Blocking phosphorylation of Rpn1-S361 leads to slowed proliferation and mitochondrial dysfunction. (PMID:31843888)
• A novel autism-associated UBLCP1 mutation impacts proteasome regulation/activity. (PMID:38129378)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ublcp1	ENSDARG00000044492
		ENSDARG00000103225
mus_musculus	Ublcp1	ENSMUSG00000041231
rattus_norvegicus	Ublcp1	ENSRNOG00000004477
drosophila_melanogaster	Ublcp1	FBGN0027526

Protein

Protein identifiers

Ubiquitin-like domain-containing CTD phosphatase 1 — Q8WVY7 (reviewed: Q8WVY7)

Alternative names: Nuclear proteasome inhibitor UBLCP1

All UniProt accessions (1): Q8WVY7

UniProt curated annotations — full annotation on UniProt →

Function. Dephosphorylates 26S nuclear proteasomes, thereby decreasing their proteolytic activity. Recruited to the 19S regulatory particle of the 26S proteasome through its interaction with 19S component PSMD2/RPN1. Once recruited, dephosphorylates 19S component PSMC2/RPT1 which impairs PSMC2 ATPase activity and disrupts 26S proteasome assembly. Has also been reported to stimulate the proteolytic activity of the 26S proteasome.

Subunit / interactions. Interacts (via ubiquitin-like domain) with PSMD2/RPN1 (via C-terminus) which is a 19S regulatory particle subunit of the 26S proteasome.

Subcellular location. Nucleus.

Tissue specificity. Broadly expressed, with highest levels in placenta, lung, testis and ovary. Up-regulated in tumor tissues.

Domain organisation. The Ubiquitin-like domain mediates interaction with proteasomes.

RefSeq proteins (1): NP_659486* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000626	Ubiquitin-like_dom	Domain
IPR004274	FCP1_dom	Domain
IPR011943	HAD-SF_hydro_IIID	Domain
IPR023214	HAD_sf	Homologous_superfamily
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR036412	HAD-like_sf	Homologous_superfamily
IPR051658	UBLCP1	Family

Pfam: PF00240, PF03031

Catalyzed reactions (Rhea), 2 shown:

• O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate (RHEA:20629)
• O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate (RHEA:47004)

UniProt features (27 total): mutagenesis site 7, strand 5, helix 3, binding site 3, turn 2, domain 2, modified residue 2, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
2KX3	SOLUTION NMR
2LGD	SOLUTION NMR
2M17	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WVY7-F1	90.51	0.78

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 (3): 143; 145; 253

Post-translational modifications (2): 2, 117

Mutagenesis-validated functional residues (7):

Position	Phenotype
44	aberrant diffuse pan-cellular localization and loss of binding to psmd2.
46	no effect on proteasome binding or nuclear localization.
49	loss of binding to psmd2 and psmc2, and loss of inhibitory effect on proteasome activity; when associated with e-51.
51	loss of binding to psmd2 and psmc2, and loss of inhibitory effect on proteasome activity; when associated with e-49.
143	loss of catalytic activity. no effect on interaction with 19s regulatory particle but loss of catalytic activity; when a
145	no effect on interaction with 19s regulatory particle but loss of catalytic activity; when associated with a-143.
10	no effect on proteasome binding or nuclear localization.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 127 (showing top): GOBP_NEGATIVE_REGULATION_OF_ATP_DEPENDENT_ACTIVITY, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_PROTEASOME_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, MARTINEZ_RB1_TARGETS_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_NEGATIVE_REGULATION_OF_MOLECULAR_FUNCTION, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_ATP_DEPENDENT_ACTIVITY, ZHANG_BREAST_CANCER_PROGENITORS_UP, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, LEIN_MIDBRAIN_MARKERS, LEIN_PONS_MARKERS, LEIN_MEDULLA_MARKERS

GO Biological Process (2): negative regulation of ATP-dependent activity (GO:0032780), regulation of proteasome assembly (GO:0090364)

GO Molecular Function (6): protein serine/threonine phosphatase activity (GO:0004722), metal ion binding (GO:0046872), proteasome regulatory particle binding (GO:1904855), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
regulation of ATP-dependent activity	1
negative regulation of molecular function	1
ATP-dependent activity	1
proteasome assembly	1
regulation of protein-containing complex assembly	1
phosphoprotein phosphatase activity	1
cation binding	1
protein-containing complex binding	1
phosphatase activity	1
catalytic activity, acting on a protein	1
binding	1
catalytic activity	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2516 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
UBLCP1	CTDP1	Q9Y5B0	873
UBLCP1	CTDSP1	Q9GZU7	815
UBLCP1	ADRM1	Q16186	705
UBLCP1	PSMD4	P55036	625
UBLCP1	PSMD11	O00231	558
UBLCP1	ARMCX5	Q6P1M9	531
UBLCP1	RNF145	Q96MT1	513
UBLCP1	ECPAS	Q5VYK3	503
UBLCP1	PSMD6	Q15008	502
UBLCP1	THG1L	Q9NWX6	488
UBLCP1	CTDSPL2	Q05D32	486
UBLCP1	USP14	P54578	477
UBLCP1	PPP4R1	Q8TF05	464
UBLCP1	RAD23A	P54725	455
UBLCP1	PSME4	Q14997	452

IntAct

77 interactions, top by confidence:

A	B	Type	Score
UBLCP1	PSMD2	psi-mi:“MI:0915”(physical association)	0.900
PSMD2	UBLCP1	psi-mi:“MI:0915”(physical association)	0.900
MED17	MED19	psi-mi:“MI:0914”(association)	0.840
PSMD2	PSMD11	psi-mi:“MI:0914”(association)	0.730
MAPT	DENR	psi-mi:“MI:0914”(association)	0.560
FSD1	UBFD1	psi-mi:“MI:0914”(association)	0.530
NUDT6	DENR	psi-mi:“MI:0914”(association)	0.530
EVA1C	STK25	psi-mi:“MI:0914”(association)	0.530
UBLCP1	RRP9	psi-mi:“MI:0915”(physical association)	0.400
CHI3L1	UBLCP1	psi-mi:“MI:0915”(physical association)	0.400
UBLCP1	TSC22D4	psi-mi:“MI:0915”(physical association)	0.370
GTF2E2	UBA6	psi-mi:“MI:0914”(association)	0.350
FGB	NME2	psi-mi:“MI:0914”(association)	0.350
UBLCP1	PSMD11	psi-mi:“MI:0914”(association)	0.350
GTF2E2	STX7	psi-mi:“MI:0914”(association)	0.350
FGB	KIF2A	psi-mi:“MI:0914”(association)	0.350
RPL35A	SMCHD1	psi-mi:“MI:0914”(association)	0.350
PRUNE2	SNX2	psi-mi:“MI:0914”(association)	0.350
MTPN	PLCG1	psi-mi:“MI:0914”(association)	0.350
LUM	CTH	psi-mi:“MI:0914”(association)	0.350
SERBP1	UBA6	psi-mi:“MI:0914”(association)	0.350

BioGRID (136): UBLCP1 (Two-hybrid), UBLCP1 (Affinity Capture-MS), UBLCP1 (Affinity Capture-MS), UBLCP1 (Two-hybrid), UBLCP1 (Two-hybrid), UBLCP1 (Co-fractionation), UBLCP1 (Co-fractionation), COLGALT1 (Affinity Capture-MS), PAAF1 (Affinity Capture-MS), PSMB2 (Affinity Capture-MS), PSMC1 (Affinity Capture-MS), PSMC2 (Affinity Capture-MS), PSMC3 (Affinity Capture-MS), PSMC4 (Affinity Capture-MS), PSMC5 (Affinity Capture-MS)

ESM2 similar proteins: A1A4Q2, A6NEY8, A6QP05, O80526, P11172, P12081, P13439, P31754, P37111, P38918, P47897, Q02053, Q16798, Q28EX9, Q2KI84, Q2KJD7, Q32LQ4, Q3MHH4, Q502H1, Q53JY8, Q5FWT7, Q5R4A0, Q5R4C4, Q5R4R2, Q5R514, Q5R8R4, Q5RGJ5, Q5U300, Q5ZJJ8, Q61035, Q641F1, Q66H61, Q6DI37, Q6DIJ1, Q6IQS6, Q6NRL0, Q7ZVX6, Q8BGR9, Q8BML9, Q8C878

Diamond homologs: A1CIL1, G5E8G2, G5E8I7, P40826, P43593, P51784, P54578, P60051, Q0CT11, Q0IIF7, Q11119, Q17361, Q24574, Q2KJD7, Q2UUG8, Q5D006, Q5FWT7, Q5R4C4, Q7M764, Q84WC6, Q8BGR9, Q8WVY7, Q92353, Q949Y0, Q99K46, Q9H0E7, Q9JMA1, D2HBJ8, E1C1R4, Q5ZJJ8, Q96V54, P0C895, Q28EX9, Q641F1, Q6DI37, Q8W3M6, Q9XZ16, F8VPZ3, O22207, O75604

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 92 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
Proteasome assembly	6	20.4×	2e-04
G2/M Checkpoints	5	11.2×	3e-03
ER-Phagosome pathway	5	10.8×	3e-03
Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide	5	8.9×	3e-03
Regulation of expression of SLITs and ROBOs	6	6.9×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1404 predictions. Top by Δscore:

Variant	Effect	Δscore
5:159268864:TTCCA:T	acceptor_gain	1.0000
5:159268865:TCCA:T	acceptor_gain	1.0000
5:159268866:CCA:C	acceptor_loss	1.0000
5:159268866:CCAGG:C	acceptor_gain	1.0000
5:159268867:CAGGT:C	acceptor_gain	1.0000
5:159268868:A:AG	acceptor_gain	1.0000
5:159268868:A:T	acceptor_gain	1.0000
5:159268868:AG:A	acceptor_gain	1.0000
5:159268869:G:C	acceptor_gain	1.0000
5:159268869:G:GG	acceptor_gain	1.0000
5:159268869:GG:G	acceptor_gain	1.0000
5:159268869:GGT:G	acceptor_gain	1.0000
5:159268869:GGTA:G	acceptor_gain	1.0000
5:159268869:GGTAT:G	acceptor_gain	1.0000
5:159269064:TTAA:T	donor_gain	1.0000
5:159269066:AAAG:A	donor_gain	1.0000
5:159269067:AAGGT:A	donor_loss	1.0000
5:159269068:AG:A	donor_gain	1.0000
5:159269069:GG:G	donor_gain	1.0000
5:159269070:G:GG	donor_gain	1.0000
5:159269070:GTA:G	donor_loss	1.0000
5:159269995:GCTTG:G	donor_gain	1.0000
5:159269996:C:G	donor_gain	1.0000
5:159270523:A:AG	acceptor_gain	1.0000
5:159270523:ATTAG:A	acceptor_gain	1.0000
5:159270524:TTAG:T	acceptor_loss	1.0000
5:159270525:TA:T	acceptor_loss	1.0000
5:159270526:A:AG	acceptor_gain	1.0000
5:159270526:AG:A	acceptor_gain	1.0000
5:159270527:G:GA	acceptor_loss	1.0000

AlphaMissense

2116 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:159268940:T:A	W9R	1.000
5:159268940:T:C	W9R	1.000
5:159268998:T:C	L28P	1.000
5:159269044:A:C	Q43H	1.000
5:159269044:A:T	Q43H	1.000
5:159269979:G:A	G76R	1.000
5:159269979:G:C	G76R	1.000
5:159269980:G:A	G76E	1.000
5:159270611:T:C	L139P	1.000
5:159270614:T:C	L140S	1.000
5:159270617:T:A	V141E	1.000
5:159270620:T:A	L142Q	1.000
5:159270620:T:C	L142P	1.000
5:159270622:G:C	D143H	1.000
5:159270623:A:C	D143A	1.000
5:159270623:A:T	D143V	1.000
5:159270624:T:A	D143E	1.000
5:159270624:T:G	D143E	1.000
5:159270628:G:C	D145H	1.000
5:159270629:A:C	D145A	1.000
5:159270629:A:G	D145G	1.000
5:159270629:A:T	D145V	1.000
5:159270630:T:A	D145E	1.000
5:159270630:T:G	D145E	1.000
5:159272061:C:G	R163G	1.000
5:159272083:T:C	L170P	1.000
5:159272118:T:A	W182R	1.000
5:159272118:T:C	W182R	1.000
5:159274591:C:T	T185I	1.000
5:159274602:T:A	W189R	1.000

dbSNP variants (sampled 300 via entrez): RS1000000285 (5:159270764 T>C), RS1000103462 (5:159263437 C>T), RS1000327778 (5:159272185 T>C), RS1000335081 (5:159280364 A>G), RS1000473698 (5:159265093 A>G,T), RS1000596837 (5:159265405 G>C), RS1000770527 (5:159274465 G>A), RS1000790995 (5:159276392 A>C), RS1000843535 (5:159276755 C>T), RS1001142223 (5:159284036 A>C), RS1001158058 (5:159262539 G>A), RS1001230448 (5:159266518 C>T), RS1001465882 (5:159279931 A>G), RS1001516868 (5:159280224 A>G), RS1001611084 (5:159282199 T>G)

Disease associations

OMIM: gene MIM:609867 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002740_44	Inflammatory skin disease	1.000000e-25
GCST003129_3	Primary biliary cholangitis	1.000000e-10
GCST003723_5	Serum sulfate level	3.000000e-06
GCST004131_19	Inflammatory bowel disease	3.000000e-38
GCST004132_14	Crohn’s disease	1.000000e-27
GCST004133_6	Ulcerative colitis	1.000000e-23
GCST005116_26	Male-pattern baldness	2.000000e-44
GCST011395_1	Tuberculosis susceptibility in HIV infection	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007864	sulfate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3317333 (SINGLE PROTEIN)

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

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acid	IC50	2900 nM	US-9522881: Hydroxyindole carboxylic acid based inhibitors for oncogenic Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2)

ChEMBL bioactivities

9 potent at pChembl≥5 of 10 total, top 9 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.30	IC50	500	nM	CHEMBL3426913
6.00	Ki	1000	nM	CHEMBL3426913
5.52	IC50	3000	nM	CHEMBL3425525
5.38	IC50	4200	nM	CHEMBL3426911
5.38	IC50	4200	nM	CHEMBL3426909
5.36	IC50	4400	nM	CHEMBL3426907
5.27	IC50	5400	nM	CHEMBL3426912
5.08	IC50	8300	nM	CHEMBL3426910
5.01	IC50	9700	nM	CHEMBL3319356

PubChem BioAssay actives

9 with measured affinity, of 13 total; 8 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-[1-(cyclohexylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-[2-[2-(trifluoromethoxy)phenyl]ethynyl]benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	0.5000	uM
4-[1-(cyclooctylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-[2-(2-methoxyphenyl)ethynyl]benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	3.0000	uM
4-[1-(cyclooctylamino)-1-oxohexan-2-yl]oxy-5-(2-cyclopentylethynyl)-2-hydroxybenzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	4.2000	uM
4-[1-(benzhydrylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-[2-[4-(hydroxymethyl)phenyl]ethynyl]benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	4.2000	uM
4-[1-(cyclooctylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-(2-thiophen-3-ylethynyl)benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	4.4000	uM
4-[1-(2,3-dihydro-1,4-benzodioxin-3-ylmethylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-[2-[3-(trifluoromethyl)phenyl]ethynyl]benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	5.4000	uM
4-[1-(cyclooctylamino)-1-oxohexan-2-yl]oxy-2-hydroxy-5-(2-phenylethynyl)benzoic acid	1206774: Inhibition of His6-tagged UBLCP1 (unknown origin) expressed in Escherichia coli BL21 cells using pNPP as substrate at pH 6 at 25 degC by spectrophotometric analysis	ic50	8.3000	uM
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acid	1182556: Inhibition of UBLCP1 (unknown origin)	ic50	9.7000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, decreases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
Valproic Acid	affects expression, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
bisphenol F	increases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
nobiletin	decreases expression, decreases reaction	1
sodium arsenate	decreases expression, decreases reaction	1
cobaltous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
bisphenol B	increases expression	1
jinfukang	decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Clorgyline	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Indomethacin	decreases expression	1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3369529	Binding	Inhibition of UBLCP1 (unknown origin)	Therapeutic potential of targeting the oncogenic SHP2 phosphatase. — 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_TW05	HAP1 UBLCP1 (-) 1	Cancer cell line	Male
CVCL_TW06	HAP1 UBLCP1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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