SSU72

Summary

SSU72 (SSU72 homolog, RNA polymerase II CTD phosphatase, HGNC:25016) is a protein-coding gene on chromosome 1p36.33, encoding RNA polymerase II subunit A C-terminal domain phosphatase SSU72 (Q9NP77). Protein phosphatase that catalyzes the dephosphorylation of the C-terminal domain of RNA polymerase II. It is a common-essential gene (DepMap: required in 99.5% of cancer cell lines).

Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in co-transcriptional mRNA 3’-end processing, cleavage and polyadenylation pathway. Located in cytosol and nucleoplasm.

Source: NCBI Gene 29101 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 20 total — 1 pathogenic
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 99.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_014188

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25016
Approved symbol	SSU72
Name	SSU72 homolog, RNA polymerase II CTD phosphatase
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	HSPC182
Ensembl gene	ENSG00000160075
Ensembl biotype	protein_coding
OMIM	617680
Entrez	29101

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000291386, ENST00000359060, ENST00000378725, ENST00000378726, ENST00000851386, ENST00000851387, ENST00000851388, ENST00000929201, ENST00000929202

RefSeq mRNA: 1 — MANE Select: NM_014188 NM_014188

CCDS: CCDS32

Canonical transcript exons

ENST00000291386 — 5 exons

Exon	Start	End
ENSE00001049594	1544863	1545002
ENSE00001478524	1574478	1574863
ENSE00001824181	1541673	1542167
ENSE00003470831	1564773	1564916
ENSE00003590028	1543869	1543987

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.84.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 150.0128 / max 716.7235, expressed in 1828 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9803	98.8398	1828
9802	33.0765	1823
9801	17.7135	1816
9793	0.1599	57
9796	0.0972	13
9797	0.0949	9
9798	0.0140	5
9795	0.0127	5
9794	0.0042	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
parotid gland	UBERON:0001831	98.84	gold quality
gastrocnemius	UBERON:0001388	98.27	gold quality
muscle of leg	UBERON:0001383	98.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.95	gold quality
gingival epithelium	UBERON:0001949	97.84	gold quality
right frontal lobe	UBERON:0002810	97.74	gold quality
right lobe of thyroid gland	UBERON:0001119	97.70	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.70	gold quality
gingiva	UBERON:0001828	97.68	gold quality
apex of heart	UBERON:0002098	97.65	gold quality
left lobe of thyroid gland	UBERON:0001120	97.64	gold quality
pancreatic ductal cell	CL:0002079	97.63	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.60	gold quality
mucosa of transverse colon	UBERON:0004991	97.54	gold quality
anterior cingulate cortex	UBERON:0009835	97.53	gold quality
caudate nucleus	UBERON:0001873	97.52	gold quality
adenohypophysis	UBERON:0002196	97.51	gold quality
thyroid gland	UBERON:0002046	97.44	gold quality
nucleus accumbens	UBERON:0001882	97.43	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.41	gold quality
primary visual cortex	UBERON:0002436	97.39	gold quality
putamen	UBERON:0001874	97.37	gold quality
right atrium auricular region	UBERON:0006631	97.33	gold quality
esophagus mucosa	UBERON:0002469	97.29	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	97.29	gold quality
prefrontal cortex	UBERON:0000451	97.24	gold quality
middle temporal gyrus	UBERON:0002771	97.22	gold quality
quadriceps femoris	UBERON:0001377	97.19	gold quality
oviduct epithelium	UBERON:0004804	97.19	gold quality
pituitary gland	UBERON:0000007	97.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting SSU72, 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-4533	100.00	69.48	2758
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 9)

• Molecular cloning and characterization of functions of human ssu72. (PMID:15659578)
• Data suggest that Ssu72 is a novel cohesin-binding protein capable of regulating cohesion between sister chromatid arms. (PMID:20818333)
• crystal structure at 2.4 A resolution of the amino-terminal domain (residues 30-340) of human symplekin in a ternary complex with the Pol II carboxy-terminal domain (CTD) Ser 5 phosphatase Ssu72 and a CTD Ser 5 phosphopeptide (PMID:20861839)
• The pSer7 phosphatase activity of Ssu72 is approximately 4000-fold lower than its pSer5 phosphatase activity toward a peptide substrate (PMID:23070812)
• Aurora B kinase directly targets Ssu72 phosphatase for regulation of sister chromatid cohesion during early mitosis. (PMID:24149858)
• a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk. (PMID:29158257)
• results demonstrate when Ssu72 can act on early transcription complexes and suggest that Ssu72 may also function in thepreinitiation complex prior to initiation. (PMID:30901332)
• Diverse and conserved roles of the protein Ssu72 in eukaryotes: from yeast to higher organisms. (PMID:33244642)
• Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases. (PMID:33917542)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ssu72	ENSDARG00000031216
mus_musculus	Ssu72	ENSMUSG00000029038
rattus_norvegicus	Ssu72	ENSRNOG00000017829
drosophila_melanogaster	Ssu72	FBGN0031054
caenorhabditis_elegans		WBGENE00020480

Paralogs (6): SSU72L6 (ENSG00000230268), SSU72L4 (ENSG00000283873), SSU72L5 (ENSG00000284018), SSU72L2 (ENSG00000284306), SSU72L1 (ENSG00000284438), SSU72L3 (ENSG00000284546)

Protein

Protein identifiers

RNA polymerase II subunit A C-terminal domain phosphatase SSU72 — Q9NP77 (reviewed: Q9NP77)

All UniProt accessions (1): Q9NP77

UniProt curated annotations — full annotation on UniProt →

Function. Protein phosphatase that catalyzes the dephosphorylation of the C-terminal domain of RNA polymerase II. Plays a role in RNA processing and termination. Plays a role in pre-mRNA polyadenylation via its interaction with SYMPK.

Subunit / interactions. Interacts with GTF2B (via C-terminus); this interaction is inhibited by SYMPK. Interacts with RB1. Interacts with CD226. Interacts with SYMPK.

Subcellular location. Nucleus. Cytoplasm.

Similarity. Belongs to the SSU72 phosphatase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NP77-1	1	yes
Q9NP77-2	2

RefSeq proteins (1): NP_054907* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006811	RNA_pol_II_suA	Family

Pfam: PF04722

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 (19 total): helix 7, strand 7, chain 1, coiled-coil region 1, splice variant 1, mutagenesis site 1, sequence conflict 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
4H3K	X-RAY DIFFRACTION	2
4H3H	X-RAY DIFFRACTION	2.2
3O2Q	X-RAY DIFFRACTION	2.4
3O2S	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NP77-F1	95.85	0.94

Functional residue map

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

Mutagenesis-validated functional residues (1):

Position	Phenotype
12	abolishes phosphatase activity.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6807505	RNA polymerase II transcribes snRNA genes
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 132 (showing top): E2F_Q4_01, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, GOBP_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN, GOBP_MRNA_3_END_PROCESSING, GARY_CD5_TARGETS_DN, GOBP_TERMINATION_OF_RNA_POLYMERASE_II_TRANSCRIPTION, FUJII_YBX1_TARGETS_DN, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS

GO Biological Process (5): termination of RNA polymerase II transcription (GO:0006369), co-transcriptional mRNA 3’-end processing, cleavage and polyadenylation pathway (GO:0180010), regulation of transcription by RNA polymerase II (GO:0006357), mRNA processing (GO:0006397), mRNA 3’-end processing (GO:0031124)

GO Molecular Function (5): RNA polymerase II CTD heptapeptide repeat phosphatase activity (GO:0008420), phosphoprotein phosphatase activity (GO:0004721), protein serine/threonine phosphatase activity (GO:0004722), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytosol (GO:0005829), mRNA cleavage and polyadenylation specificity factor complex (GO:0005847), nucleus (GO:0005634), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
transcription by RNA polymerase II	2
DNA-templated transcription termination	1
mRNA 3’-end processing	1
co-transcriptional RNA 3’-end processing, cleavage and polyadenylation pathway	1
regulation of DNA-templated transcription	1
RNA processing	1
mRNA metabolic process	1
mRNA processing	1
RNA 3’-end processing	1
protein serine/threonine phosphatase activity	1
RNA polymerase II CTD heptapeptide repeat modifying activity	1
phosphatase activity	1
catalytic activity, acting on a protein	1
phosphoprotein phosphatase activity	1
binding	1
catalytic activity	1
nuclear lumen	1
cytoplasm	1
mRNA cleavage factor complex	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1812 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSU72	WDR82	Q6UXN9	980
SSU72	GTF2B	Q00403	936
SSU72	CPSF3	Q9UKF6	885
SSU72	PCF11	O94913	873
SSU72	SYMPK	Q92797	861
SSU72	CTDP1	Q9Y5B0	821
SSU72	RPAP2	Q8IXW5	810
SSU72	EEF1A1	P04719	798
SSU72	POLR2B	P30876	787
SSU72	SUPT5H	O00267	774
SSU72	CD226	Q15762	745
SSU72	CPSF2	Q9P2I0	717
SSU72	CSTF2	P33240	714
SSU72	WDR33	Q9C0J8	705
SSU72	POLR2A	P24928	638

IntAct

27 interactions, top by confidence:

A	B	Type	Score
RAD21	STAG2	psi-mi:“MI:0914”(association)	0.970
RAD21	SMC1A	psi-mi:“MI:0914”(association)	0.930
SSU72	RAD21	psi-mi:“MI:0915”(physical association)	0.670
SSU72	RAD21	psi-mi:“MI:0914”(association)	0.670
RAD21	SSU72	psi-mi:“MI:0407”(direct interaction)	0.670
SSU72	RAD21	psi-mi:“MI:0403”(colocalization)	0.670
STAG2	SSU72	psi-mi:“MI:0407”(direct interaction)	0.580
HTT	SSU72	psi-mi:“MI:0915”(physical association)	0.560
CPSF6	DDX39A	psi-mi:“MI:0914”(association)	0.480
MAPK8	SSU72	psi-mi:“MI:0915”(physical association)	0.370
SSU72	MAPK9	psi-mi:“MI:0915”(physical association)	0.370
FOS	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
UIMC1	PYCR3	psi-mi:“MI:0914”(association)	0.350
SSU72	HNRNPL	psi-mi:“MI:0914”(association)	0.350
SPANXN4	UBA6	psi-mi:“MI:0914”(association)	0.350
EN1	MEIS1	psi-mi:“MI:0914”(association)	0.350
PRM3	ARRB2	psi-mi:“MI:0914”(association)	0.350
POU3F1	DUSP3	psi-mi:“MI:0914”(association)	0.350
EPB41L5	LIN7A	psi-mi:“MI:0914”(association)	0.350
SSU72	PCF11	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (79): SSU72 (Co-fractionation), SSU72 (Co-fractionation), SSU72 (Co-fractionation), SSU72 (Co-fractionation), SSU72 (Co-fractionation), SSU72 (Affinity Capture-MS), CPSF1 (Affinity Capture-MS), CPSF2 (Affinity Capture-MS), CPSF3 (Affinity Capture-MS), CSTF2 (Affinity Capture-MS), CSTF3 (Affinity Capture-MS), HIST2H2AA4 (Affinity Capture-MS), HNRNPL (Affinity Capture-MS), SYMPK (Affinity Capture-MS), CDKN2AIP (Proximity Label-MS)

ESM2 similar proteins: A0JN27, A6H7F7, B2RYU6, B5FXJ6, B5FYY5, B5X7X4, F1LTR1, F6RQL9, O14787, O43504, P22234, P61201, P61202, P61203, Q13126, Q13888, Q17QI2, Q2TBV5, Q2YDH6, Q3SZ68, Q3T132, Q4KLK9, Q4R9A8, Q4VC33, Q5F398, Q5R532, Q5RKJ1, Q5SP67, Q5ZJQ7, Q63ZJ2, Q66X52, Q6DEG4, Q6DF40, Q6IQT4, Q6IR75, Q6P1K8, Q7L5Y9, Q7ZXB7, Q92572, Q99LG2

Diamond homologs: A0A1W2PQ27, A0A1W2PQ64, A0A1W2PQC6, A0A1W2PQD8, A0A1W2PQJ5, A0A1W2PR75, O42868, P0CR76, P0CR77, P53538, Q17QI2, Q22453, Q2HFZ9, Q2UPU5, Q4IPC8, Q4KLK9, Q4WHY5, Q558Z3, Q5ZJQ7, Q6BYP7, Q6C195, Q6CQ61, Q6FMU7, Q6NRQ7, Q6PC19, Q75E60, Q7SFY0, Q9CY97, Q9NP77

SIGNOR signaling

27 interactions.

A	Effect	B	Mechanism
SSU72	“up-regulates activity”	POLR2A	dephosphorylation
AURKB	“down-regulates quantity by destabilization”	SSU72	phosphorylation
AURKB	“down-regulates activity”	SSU72	phosphorylation
SSU72	“up-regulates activity”	STAG2	dephosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	12
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1328099	GRCh37/hg19 1p36.33-36.32(chr1:753552-4034574)x1	Pathogenic

SpliceAI

1343 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1542168:C:CC	acceptor_gain	1.0000
1:1542168:CTGC:C	acceptor_loss	1.0000
1:1543863:ACTT:A	donor_loss	1.0000
1:1543867:A:AC	donor_gain	1.0000
1:1543867:A:T	donor_loss	1.0000
1:1543868:C:CC	donor_gain	1.0000
1:1543868:CA:C	donor_gain	1.0000
1:1543868:CACA:C	donor_gain	1.0000
1:1543983:CAGAT:C	acceptor_gain	1.0000
1:1543984:AGAT:A	acceptor_gain	1.0000
1:1543986:AT:A	acceptor_gain	1.0000
1:1543988:C:CC	acceptor_gain	1.0000
1:1543988:C:T	acceptor_loss	1.0000
1:1543989:T:G	acceptor_loss	1.0000
1:1552031:C:A	donor_gain	1.0000
1:1564786:T:A	donor_gain	1.0000
1:1564805:CAT:C	donor_gain	1.0000
1:1564917:C:CC	acceptor_gain	1.0000
1:1542163:TGGAT:T	acceptor_gain	0.9900
1:1542165:GAT:G	acceptor_gain	0.9900
1:1542166:AT:A	acceptor_gain	0.9900
1:1543862:TAC:T	donor_loss	0.9900
1:1543865:TTA:T	donor_gain	0.9900
1:1543865:TTACA:T	donor_gain	0.9900
1:1543866:TAC:T	donor_gain	0.9900
1:1543866:TACAC:T	donor_gain	0.9900
1:1543867:ACA:A	donor_gain	0.9900
1:1543867:ACACA:A	donor_gain	0.9900
1:1543868:CAC:C	donor_gain	0.9900
1:1543868:CACAC:C	donor_gain	0.9900

AlphaMissense

1299 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:1543897:G:T	A152E	1.000
1:1543900:C:T	G151E	1.000
1:1543901:C:A	G151W	1.000
1:1543901:C:G	G151R	1.000
1:1543901:C:T	G151R	1.000
1:1543909:G:T	A148D	1.000
1:1543910:C:G	A148P	1.000
1:1543923:G:C	D143E	1.000
1:1543923:G:T	D143E	1.000
1:1543924:T:A	D143V	1.000
1:1543924:T:C	D143G	1.000
1:1543924:T:G	D143A	1.000
1:1543925:C:A	D143Y	1.000
1:1543925:C:G	D143H	1.000
1:1543925:C:T	D143N	1.000
1:1543938:A:C	N138K	1.000
1:1543938:A:T	N138K	1.000
1:1543945:A:T	V136E	1.000
1:1544894:G:C	C111W	1.000
1:1544895:C:T	C111Y	1.000
1:1544934:A:G	F98S	1.000
1:1544943:G:T	P95Q	1.000
1:1544944:G:A	P95S	1.000
1:1544951:C:A	K92N	1.000
1:1544951:C:G	K92N	1.000
1:1544953:T:C	K92E	1.000
1:1544963:A:C	N88K	1.000
1:1544963:A:T	N88K	1.000
1:1544966:T:A	R87S	1.000
1:1544966:T:G	R87S	1.000

dbSNP variants (sampled 300 via entrez): RS1000033034 (1:1573494 G>A,C), RS1000033620 (1:1559802 C>T), RS1000143929 (1:1558293 G>C), RS1000209096 (1:1555670 C>A), RS1000224402 (1:1542576 A>G), RS1000254452 (1:1553996 G>A,C), RS1000278304 (1:1542792 A>C), RS1000333653 (1:1564351 A>C,T), RS1000340266 (1:1568539 G>A), RS1000363165 (1:1558090 T>C), RS1000384168 (1:1573684 T>C), RS1000497265 (1:1557238 T>A,C,G), RS1000515570 (1:1546488 A>C,T), RS1000613929 (1:1541939 A>G), RS1000715530 (1:1556985 T>C)

Disease associations

OMIM: gene MIM:617680 | disease phenotypes: MIM:611490

GenCC curated gene-disease

Mondo (1): autosomal recessive osteopetrosis 4 (MONDO:0012676)

Orphanet (1): Autosomal recessive malignant osteopetrosis (Orphanet:667)

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005951_34	Body mass index	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C566933	Osteopetrosis, Autosomal Recessive 4 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3317331 (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

1 potent at pChembl≥5 of 4 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.89	IC50	1300	nM	CHEMBL3319356

PubChem BioAssay actives

1 with measured affinity, of 13 total; 1 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
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acid	1182545: Inhibition of Ssu72 (unknown origin)	ic50	1.3000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	5
bisphenol A	increases methylation, increases expression, affects cotreatment	2
sodium arsenite	decreases expression	2
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
monomethylarsonous acid	decreases 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
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
eprenetapopt	affects expression, affects reaction	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Arsenic	affects expression, affects methylation	1
Catechin	increases expression, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Phthalic Acids	increases methylation	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Sodium Selenite	increases expression	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3369287	Binding	Inhibition of Ssu72 (unknown origin)	Therapeutic potential of targeting the oncogenic SHP2 phosphatase. — J Med Chem

Clinical trials (associated diseases)

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