RPS25

Summary

RPS25 (ribosomal protein S25, HGNC:10413) is a protein-coding gene on chromosome 11q23.3, encoding Small ribosomal subunit protein eS25 (P62851). Component of the small ribosomal subunit. It is a common-essential gene (DepMap: required in 99.6% of cancer cell lines).

Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit. The protein belongs to the S25E family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.

Source: NCBI Gene 6230 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 12 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_001028

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10413
Approved symbol	RPS25
Name	ribosomal protein S25
Location	11q23.3
Locus type	gene with protein product
Status	Approved
Aliases	S25, eS25
Ensembl gene	ENSG00000118181
Ensembl biotype	protein_coding
OMIM	180465
Entrez	6230

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000524864, ENST00000527673, ENST00000527791, ENST00000527853, ENST00000528547, ENST00000532567, ENST00000891654, ENST00000891655, ENST00000937795, ENST00000937796, ENST00000937797, ENST00000937798, ENST00000937799, ENST00000937800, ENST00000942362

RefSeq mRNA: 1 — MANE Select: NM_001028 NM_001028

CCDS: CCDS8406

Canonical transcript exons

ENST00000527673 — 5 exons

Exon	Start	End
ENSE00001275591	119017958	119018053
ENSE00002144944	119018282	119018343
ENSE00003480940	119017362	119017545
ENSE00003512878	119015841	119015939
ENSE00003849338	119015717	119015758

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1453.2492 / max 17964.4060, expressed in 1827 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
122655	1442.4437	1827
122656	9.2577	1671
122654	1.4087	655
122653	0.1390	38

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	99.94	gold quality
ovary	UBERON:0000992	99.93	gold quality
right ovary	UBERON:0002118	99.93	gold quality
pituitary gland	UBERON:0000007	99.92	gold quality
right uterine tube	UBERON:0001302	99.92	gold quality
adenohypophysis	UBERON:0002196	99.92	gold quality
calcaneal tendon	UBERON:0003701	99.92	gold quality
mucosa of stomach	UBERON:0001199	99.91	gold quality
fallopian tube	UBERON:0003889	99.91	gold quality
lymph node	UBERON:0000029	99.90	gold quality
endocervix	UBERON:0000458	99.90	gold quality
right lobe of thyroid gland	UBERON:0001119	99.90	gold quality
left lobe of thyroid gland	UBERON:0001120	99.90	gold quality
right coronary artery	UBERON:0001625	99.90	gold quality
thyroid gland	UBERON:0002046	99.90	gold quality
subcutaneous adipose tissue	UBERON:0002190	99.90	gold quality
thoracic mammary gland	UBERON:0005200	99.90	gold quality
adipose tissue	UBERON:0001013	99.89	gold quality
left uterine tube	UBERON:0001303	99.89	gold quality
popliteal artery	UBERON:0002250	99.89	gold quality
tibial artery	UBERON:0007610	99.89	gold quality
omental fat pad	UBERON:0010414	99.89	gold quality
ectocervix	UBERON:0012249	99.89	gold quality
muscle layer of sigmoid colon	UBERON:0035805	99.89	gold quality
fundus of stomach	UBERON:0001160	99.88	gold quality
tibial nerve	UBERON:0001323	99.88	gold quality
ascending aorta	UBERON:0001496	99.88	gold quality
thoracic aorta	UBERON:0001515	99.88	gold quality
left coronary artery	UBERON:0001626	99.88	gold quality
gall bladder	UBERON:0002110	99.88	gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	39.82
E-MTAB-9067	yes	29.03
E-HCAD-35	yes	7.86
E-MTAB-9801	yes	6.09
E-GEOD-70580	no	1464.62
E-CURD-97	no	1415.16
E-GEOD-76312	no	1253.26
E-MTAB-6075	no	936.65
E-MTAB-9388	no	808.77
E-MTAB-7606	no	681.45
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 4)

• data demonstrate that ribosomal protein S25 is a novel regulator of the MDM2-p53 circuit in ribosomal stress; results shed light on biological consequences of RP-MDM2-p53 interplay and also reveal the existence of a novel S25-p53 feedback regulatory loop (PMID:22777350)
• HBZ induces nuclear retention of RPS25 mRNA in the nucleus and loss of RPS25 protein expression. Inhibition of RPS25 expression stimulates Delta JunD synthesis. (PMID:28260789)
• We performed a genetic screen for regulators of RAN translation and identified small ribosomal protein subunit 25 (RPS25), presenting a potential therapeutic target for C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia and other neurodegenerative diseases caused by nucleotide repeat expansions. (PMID:31358992)
• A memory of eS25 loss drives resistance phenotypes. (PMID:32463448)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rps25	ENSDARG00000041811
rattus_norvegicus	Rps25l3	ENSRNOG00000062325
drosophila_melanogaster	RpS25	FBGN0086472
caenorhabditis_elegans		WBGENE00004494

Protein

Protein identifiers

Small ribosomal subunit protein eS25 — P62851 (reviewed: P62851)

Alternative names: 40S ribosomal protein S25

All UniProt accessions (3): P62851, E9PK60, E9PQK3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the small ribosomal subunit. The ribosome is a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.

Subunit / interactions. Component of the small ribosomal subunit.

Subcellular location. Cytoplasm.

Similarity. Belongs to the eukaryotic ribosomal protein eS25 family.

RefSeq proteins (1): NP_001019* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004977	Ribosomal_eS25	Family
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily

Pfam: PF03297

UniProt features (19 total): modified residue 7, strand 4, helix 4, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

209 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8GLP	ELECTRON MICROSCOPY	1.67
8QOI	ELECTRON MICROSCOPY	1.9
9O3W	ELECTRON MICROSCOPY	1.9
8YOO	ELECTRON MICROSCOPY	2
9C3H	ELECTRON MICROSCOPY	2
7R4X	ELECTRON MICROSCOPY	2.15
9I2D	ELECTRON MICROSCOPY	2.19
9PBE	ELECTRON MICROSCOPY	2.19
8YOP	ELECTRON MICROSCOPY	2.2
9O3V	ELECTRON MICROSCOPY	2.2
9O3Y	ELECTRON MICROSCOPY	2.2
8JDK	ELECTRON MICROSCOPY	2.26
8G5Y	ELECTRON MICROSCOPY	2.29
9S3D	ELECTRON MICROSCOPY	2.32
9RPV	ELECTRON MICROSCOPY	2.35
9S3B	ELECTRON MICROSCOPY	2.38
8K2C	ELECTRON MICROSCOPY	2.4
8XSX	ELECTRON MICROSCOPY	2.4
9SPF	ELECTRON MICROSCOPY	2.4
9SPI	ELECTRON MICROSCOPY	2.4
8JDL	ELECTRON MICROSCOPY	2.42
9S3C	ELECTRON MICROSCOPY	2.42
9QLO	ELECTRON MICROSCOPY	2.47
9P8B	ELECTRON MICROSCOPY	2.48
7XNY	ELECTRON MICROSCOPY	2.5
8JDJ	ELECTRON MICROSCOPY	2.5
9RUC	ELECTRON MICROSCOPY	2.5
8G60	ELECTRON MICROSCOPY	2.54
8IFE	ELECTRON MICROSCOPY	2.57
9P7D	ELECTRON MICROSCOPY	2.57

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62851-F1	74.36	0.34

Functional residue map

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

Post-translational modifications (7): 94, 43, 52, 52, 60, 66, 94

Function

Pathways and Gene Ontology

Reactome pathways

50 pathways

ID	Pathway
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression
R-HSA-156902	Peptide chain elongation
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane
R-HSA-192823	Viral mRNA Translation
R-HSA-2408557	Selenocysteine synthesis
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72649	Translation initiation complex formation
R-HSA-72689	Formation of a pool of free 40S subunits
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex
R-HSA-72702	Ribosomal scanning and start codon recognition
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit
R-HSA-72764	Eukaryotic Translation Termination
R-HSA-9010553	Regulation of expression of SLITs and ROBOs
R-HSA-9633012	Response of EIF2AK4 (GCN2) to amino acid deficiency
R-HSA-9735869	SARS-CoV-1 modulates host translation machinery
R-HSA-9754678	SARS-CoV-2 modulates host translation machinery
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-HSA-9954714	PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA
R-HSA-9954716	ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA
R-HSA-1266738	Developmental Biology
R-HSA-1430728	Metabolism
R-HSA-156842	Eukaryotic Translation Elongation
R-HSA-1643685	Disease
R-HSA-168255	Influenza Infection
R-HSA-168273	Influenza Viral RNA Transcription and Replication
R-HSA-2262752	Cellular responses to stress
R-HSA-2408522	Selenoamino acid metabolism
R-HSA-376176	Signaling by ROBO receptors
R-HSA-392499	Metabolism of proteins

MSigDB gene sets: 225 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, GOBP_RIBOSOME_BIOGENESIS, MODULE_151, MORF_UBE2I, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, HSIAO_HOUSEKEEPING_GENES, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_TRANSLATION, MARTINEZ_RB1_TARGETS_DN, GOBP_RIBOSOMAL_SMALL_SUBUNIT_BIOGENESIS, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GNF2_FBL, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, ACTTTAT_MIR1425P

GO Biological Process (4): cytoplasmic translation (GO:0002181), rRNA processing (GO:0006364), translation (GO:0006412), ribosomal small subunit biogenesis (GO:0042274)

GO Molecular Function (3): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (13): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), ribosome (GO:0005840), postsynaptic density (GO:0014069), small ribosomal subunit (GO:0015935), cytosolic ribosome (GO:0022626), cytosolic small ribosomal subunit (GO:0022627), extracellular exosome (GO:0070062), synapse (GO:0045202), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Cap-dependent Translation Initiation	4
Translation	2
Nonsense-Mediated Decay (NMD)	2
Ribosome-associated quality control	2
Eukaryotic Translation Initiation	1
Eukaryotic Translation Elongation	1
Influenza Viral RNA Transcription and Replication	1
Selenoamino acid metabolism	1
rRNA processing in the nucleus and cytosol	1
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	1
Signaling by ROBO receptors	1
Cellular response to starvation	1
SARS-CoV-1-host interactions	1
SARS-CoV-2-host interactions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
ribosome biogenesis	2
ribosome	2
nuclear lumen	2
intracellular membraneless organelle	2
translation	1
RNA processing	1
rRNA metabolic process	1
peptidyltransferase activity	1
translational initiation	1
translational elongation	1
translational termination	1
macromolecule biosynthetic process	1
protein metabolic process	1
protein biosynthetic process	1
ribonucleoprotein complex biogenesis	1
nucleic acid binding	1
structural molecule activity	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1
asymmetric synapse	1
postsynaptic specialization	1
ribosomal subunit	1
cytosol	1
small ribosomal subunit	1
cytosolic ribosome	1
extracellular vesicle	1
cell junction	1
protein-containing complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

280 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
NCBP2	KPNA3	psi-mi:“MI:0914”(association)	0.640
RACK1	RPS17	psi-mi:“MI:0915”(physical association)	0.610
THAP1	RPS25	psi-mi:“MI:0915”(physical association)	0.560
RPS25	THAP1	psi-mi:“MI:0915”(physical association)	0.560
RPS25	TSPYL2	psi-mi:“MI:0915”(physical association)	0.560
	RPS25	psi-mi:“MI:0915”(physical association)	0.560
ZBTB14	RPS25	psi-mi:“MI:0915”(physical association)	0.560
RPS25	HMBOX1	psi-mi:“MI:0915”(physical association)	0.560
RPS25	STAC3	psi-mi:“MI:0915”(physical association)	0.560
RPS25	NKAPD1	psi-mi:“MI:0915”(physical association)	0.560
RPS25	E7	psi-mi:“MI:0915”(physical association)	0.550
RPL13	RPLP1	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
FUS	DDX3X	psi-mi:“MI:0914”(association)	0.430
MAP3K4	RPS25	psi-mi:“MI:0915”(physical association)	0.400
RPS25	RPS5	psi-mi:“MI:0915”(physical association)	0.400
RPS25	RPS19	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (606): RPS25 (Affinity Capture-MS), THAP1 (Two-hybrid), RPS25 (Affinity Capture-MS), RPS25 (Affinity Capture-MS), RPS25 (Affinity Capture-MS), RPS25 (Affinity Capture-MS), RPS25 (Affinity Capture-MS), FAU (Co-fractionation), HNRNPU (Co-fractionation), RPL10 (Co-fractionation), RPL10A (Co-fractionation), RPL12 (Co-fractionation), RPL13 (Co-fractionation), RPL13A (Co-fractionation), RPL15 (Co-fractionation)

ESM2 similar proteins: A0A1D8PNQ6, G1TDB3, J9PAS6, O61749, O74172, P05749, P09132, P0C0T4, P0CX49, P0CX50, P14327, P34264, P37164, P37165, P48588, P49181, P52821, P56628, P62851, P62852, P62853, P79009, Q03409, Q09817, Q3E792, Q3ZBG7, Q4WX89, Q54VN6, Q54VZ4, Q56JX5, Q5B8Y4, Q5RBR1, Q6FPX5, Q6PBI5, Q6Q311, Q75DJ1, Q7SC06, Q8AVP1, Q8ISN9, Q8STD9

Diamond homologs: A0A1D8PNQ6, G1TDB3, O74172, P0C0T4, P46301, P48588, P52821, P62851, P62852, P62853, P79009, Q03409, Q3E792, Q56JX5, Q6FPX5, Q6PBI5, Q6Q311, Q75DJ1, Q7SC06, Q8GYL5, Q8ISN9, Q90YP9, Q94G66, Q962Q5, Q9N9V4, Q9SIK2, Q9SIW5, Q9T029, Q975P8, Q97ZZ6, Q8STD9

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RPS25	“form complex”	“40S cytosolic small ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 194 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
Eukaryotic Translation Initiation	9	20.7×	8e-09
Cap-dependent Translation Initiation	9	20.7×	8e-09
SARS-CoV-1 modulates host translation machinery	9	20.7×	8e-09
Formation of the ternary complex, and subsequently, the 43S complex	12	19.3×	3e-11
Eukaryotic Translation Elongation	9	18.7×	2e-08
Ribosomal scanning and start codon recognition	13	18.5×	6e-12
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	9	18.3×	2e-08
Nonsense-Mediated Decay (NMD)	10	17.4×	6e-09

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	20	21.8×	2e-18
stress granule assembly	5	17.7×	9e-04
translational initiation	8	16.9×	5e-06
ribosomal small subunit biogenesis	10	13.4×	1e-06
ribosomal large subunit biogenesis	5	13.0×	4e-03
mRNA stabilization	6	12.9×	8e-04
stem cell population maintenance	5	12.4×	4e-03
translation	20	12.1×	2e-13

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

573 predictions. Top by Δscore:

Variant	Effect	Δscore
11:119015936:AGTC:A	acceptor_gain	1.0000
11:119015937:GTCC:G	acceptor_loss	1.0000
11:119015938:TC:T	acceptor_gain	1.0000
11:119015939:CC:C	acceptor_gain	1.0000
11:119015940:C:CC	acceptor_gain	1.0000
11:119015940:CT:C	acceptor_loss	1.0000
11:119015941:T:G	acceptor_loss	1.0000
11:119017356:CCTCA:C	donor_loss	1.0000
11:119017357:CTCA:C	donor_loss	1.0000
11:119017358:TCA:T	donor_loss	1.0000
11:119017360:ACCTT:A	donor_loss	1.0000
11:119017541:CACTT:C	acceptor_gain	1.0000
11:119017551:C:CT	acceptor_gain	1.0000
11:119017554:C:T	acceptor_gain	1.0000
11:119017960:T:A	donor_gain	1.0000
11:119018277:CTTA:C	donor_loss	1.0000
11:119018280:A:AC	donor_gain	1.0000
11:119018281:C:CC	donor_gain	1.0000
11:119018281:C:CG	donor_loss	1.0000
11:119015532:TTTCA:T	acceptor_loss	0.9900
11:119015533:TTCA:T	acceptor_loss	0.9900
11:119015534:TCA:T	acceptor_loss	0.9900
11:119015535:CAG:C	acceptor_loss	0.9900
11:119015536:A:AC	acceptor_loss	0.9900
11:119015536:A:AG	acceptor_gain	0.9900
11:119015537:G:GG	acceptor_gain	0.9900
11:119015537:GAC:G	acceptor_gain	0.9900
11:119015935:AAGTC:A	acceptor_gain	0.9900
11:119015937:GTC:G	acceptor_gain	0.9900
11:119017361:CCT:C	donor_gain	0.9900

AlphaMissense

807 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:119015890:T:A	R111S	1.000
11:119015890:T:G	R111S	1.000
11:119015891:C:A	R111I	1.000
11:119015900:A:T	I108N	1.000
11:119017373:A:G	L91P	1.000
11:119017385:G:T	A87D	1.000
11:119017394:G:T	A84D	1.000
11:119017397:A:G	L83P	1.000
11:119017403:C:T	G81D	1.000
11:119017404:C:G	G81R	1.000
11:119017409:A:T	I79N	1.000
11:119017411:C:A	K78N	1.000
11:119017411:C:G	K78N	1.000
11:119017413:T:C	K78E	1.000
11:119017415:A:G	L77P	1.000
11:119017417:T:A	R76S	1.000
11:119017417:T:G	R76S	1.000
11:119017418:C:A	R76I	1.000
11:119017418:C:G	R76T	1.000
11:119017421:T:A	E75V	1.000
11:119017422:C:T	E75K	1.000
11:119017424:G:A	S74F	1.000
11:119017427:A:T	V73D	1.000
11:119017433:G:T	A71D	1.000
11:119017439:G:A	T69I	1.000
11:119017442:A:C	I68R	1.000
11:119017442:A:T	I68K	1.000
11:119017445:A:G	L67P	1.000
11:119017447:T:A	K66N	1.000
11:119017447:T:G	K66N	1.000

dbSNP variants (sampled 300 via entrez): RS1000121364 (11:119015770 A>G), RS1000708180 (11:119019907 A>G), RS1000730956 (11:119017219 G>A,C,T), RS1001022384 (11:119018706 G>A,C,T), RS1001474460 (11:119018506 A>G), RS1001527529 (11:119017265 T>A,C), RS1001558402 (11:119017693 A>G), RS1001746295 (11:119016060 G>A), RS1003027653 (11:119016902 G>A,C), RS1003273212 (11:119018458 A>C,T), RS1004842040 (11:119017305 T>C), RS1004952670 (11:119016710 C>G), RS1005472286 (11:119018497 A>G), RS1006280700 (11:119018234 A>G), RS1008132113 (11:119016597 C>A,T)

Disease associations

OMIM: gene MIM:180465 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (2): CHEMBL3987582 (PROTEIN NUCLEIC-ACID COMPLEX), CHEMBL6067565 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds).

Molecule	Name	Phase	Patents
CHEMBL6067484	GENTAMICIN SULFATE	4

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

ChEMBL bioactivities

50 potent at pChembl≥5 of 54 total, top 49 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.70	Kd	200.1	nM	CHEMBL5653589
6.70	ED50	200.1	nM	CHEMBL5653589
6.52	IC50	300	nM	CHEMBL4109308
6.42	IC50	380	nM	CHEMBL4109308
6.42	IC50	380	nM	CHEMBL4574496
6.41	IC50	390	nM	CHEMBL4126894
6.39	IC50	410	nM	CHEMBL4114159
6.35	IC50	450	nM	CHEMBL4126496
6.30	IC50	500	nM	CHEMBL4574496
6.30	IC50	500	nM	CHEMBL4560206
6.16	IC50	690	nM	CHEMBL4130157
6.15	IC50	710	nM	CHEMBL4108338
6.11	IC50	780	nM	CHEMBL4114159
6.09	IC50	820	nM	CHEMBL4109308
6.07	IC50	850	nM	CHEMBL4107559
6.07	IC50	850	nM	CHEMBL4533299
6.05	IC50	900	nM	CHEMBL4126894
6.05	IC50	900	nM	CHEMBL4126496
6.04	IC50	920	nM	CHEMBL4554909
5.97	IC50	1060	nM	CHEMBL4128388
5.89	IC50	1290	nM	CHEMBL4130157
5.86	IC50	1370	nM	CHEMBL4107559
5.84	IC50	1440	nM	CHEMBL4108338
5.81	IC50	1540	nM	CHEMBL4534859
5.76	IC50	1730	nM	CHEMBL4534859
5.69	IC50	2050	nM	CHEMBL4566239
5.68	IC50	2080	nM	CHEMBL4446635
5.66	IC50	2210	nM	CHEMBL4446635
5.66	EC50	2200	nM	CHEMBL4464929
5.64	IC50	2270	nM	CHEMBL4533299
5.63	IC50	2330	nM	CHEMBL4566239
5.62	IC50	2380	nM	CHEMBL4128388
5.58	IC50	2630	nM	CHEMBL4128250
5.58	Kd	2635	nM	CHEMBL3752910
5.58	ED50	2635	nM	CHEMBL3752910
5.55	IC50	2820	nM	CHEMBL4127458
5.53	IC50	2970	nM	CHEMBL4127311
5.51	IC50	3080	nM	CHEMBL4126072
5.46	IC50	3500	nM	CHEMBL4525277
5.44	IC50	3630	nM	CHEMBL4469712
5.39	IC50	4100	nM	CHEMBL4128560
5.37	IC50	4300	nM	CHEMBL4127016
5.36	IC50	4380	nM	CHEMBL4527910
5.16	IC50	7000	nM	CHEMBL4109308
5.13	IC50	7400	nM	CHLORAMPHENICOL SULFATE SALT
5.09	IC50	8040	nM	CHEMBL4128250
5.08	IC50	8370	nM	CHEMBL4128250
5.03	IC50	9320	nM	CHEMBL4127016
5.03	IC50	9240	nM	CHEMBL4128560

PubChem BioAssay actives

48 with measured affinity, of 209 total; 28 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	2149298: Binding affinity to human RPS25 incubated for 45 mins by Kinobead based pull down assay	kd	0.2001	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide	1585498: Binding affinity to 80S ribosome in human HuH7 cells expressing human C-terminal V5/6-His-tagged PCSK9 assessed as inhibition of PCSK9 secretion after 16 to 24 hrs by AlphaLISA method	ic50	0.3000	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-3-[4-(triazolo[4,5-b]pyridin-3-yl)phenyl]propanamide	1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.3800	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-(triazolo[4,5-b]pyridin-3-yl)benzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.3900	uM
N-(3-chloro-2-pyridinyl)-4-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.4100	uM
N-(3-chloro-2-pyridinyl)-4-(5-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.4500	uM
N-(1-methylpyrrolo[2,3-c]pyridin-7-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	0.5000	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylbenzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.6900	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-5-(triazolo[4,5-b]pyridin-3-yl)pyridine-2-carboxamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.7100	uM
N-(3-chloro-2-pyridinyl)-3-[5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-2-pyridinyl]-N-[(3R)-piperidin-3-yl]propanamide	1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.8500	uM
N-(3-chloro-2-pyridinyl)-5-(6-methyltriazolo[4,5-b]pyridin-3-yl)-N-[(3R)-piperidin-3-yl]pyridine-2-carboxamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	0.8500	uM
N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-4-pyrazolo[1,5-a]pyrimidin-3-ylpiperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	0.9200	uM
N-isoquinolin-1-yl-4-(1-methylpyrazol-4-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	1.0600	uM
N-isoquinolin-1-yl-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	1.5400	uM
N-(3-methyl-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	2.0500	uM
N-(3-chloro-2-pyridinyl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	2.0800	uM
N-(5,8-dihydroisoquinolin-1-yl)-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide	1584424: Inhibition of human 80S ribosome-mediated PCSK9 translation expressed in CHO-K1 cells assessed as reduction in PCSK9 secretion	ec50	2.2000	uM
N-isoquinolin-1-yl-3-(4-methoxyphenyl)-N-[(3R)-piperidin-3-yl]propanamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	2.6300	uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149298: Binding affinity to human RPS25 incubated for 45 mins by Kinobead based pull down assay	kd	2.6350	uM
N-(3-chloro-2-pyridinyl)-4-(6-methylpyrazin-2-yl)-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	2.8200	uM
N-(3-chloro-2-pyridinyl)-4-[6-(dimethylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	2.9700	uM
N-(3-chloro-2-pyridinyl)-4-[6-(methylamino)pyrazin-2-yl]-N-[(3R)-piperidin-3-yl]benzamide	1497963: Binding affinity to 80S ribosome in human HuH7 cells assessed as inhibition of PCSK9 mRNA translation after overnight incubation by ELISA	ic50	3.0800	uM
N-isoquinolin-1-yl-4-(6-methyl-1,2-benzoxazol-3-yl)-N-[(3R)-piperidin-3-yl]piperazine-1-carboxamide	1532845: Binding affinity to 80S ribosome in human HuH7 cells harboring human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	3.5000	uM
N-(3-methylpyrazin-2-yl)-4-phenyl-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	3.6300	uM
N-(3-chloro-2-pyridinyl)-N-[(3R)-piperidin-3-yl]-6-(triazolo[4,5-b]pyridin-3-yl)pyridine-3-carboxamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	4.1000	uM
N-isoquinolin-1-yl-N-[(3R)-piperidin-3-yl]-4-pyrazin-2-ylbenzamide	1497947: Binding affinity to 80S ribosome in human HuH7 cells harboring pCMV-truncated human PCSK9 (1 to 152 residues)-proLuc assessed as inhibition of PCSK9 mRNA translation after overnight incubation by luciferase reporter gene assay	ic50	4.3000	uM
4-(2-fluorophenyl)-N-(3-methyl-2-pyridinyl)-N-[(3R)-piperidin-3-yl]piperidine-1-carboxamide	1532846: Binding affinity to 80S ribosome in human HeLa cells lysates using human full length PCSK9 encoding mRNAs assessed as inhibition of PCSK9 mRNA translation after 45 mins by Steady-Glo luciferase reporter gene assay	ic50	4.3800	uM
2,2-dichloro-N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]acetamide;sulfuric acid	717551: Inhibition of mitochondrial ribosome-mediated protein synthesis in human HeLa cells assessed as {35S]methionine incorporation by autoradiography	ic50	7.4000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases activity, increases abundance	5
bisphenol A	decreases expression	2
Arsenic Trioxide	decreases expression, increases expression	2
Arsenic	affects cotreatment, decreases expression, increases abundance	2
bisphenol F	increases expression	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
perfluorooctanoic acid	decreases expression	1
arsenic trichloride	affects cotreatment, decreases expression, increases abundance	1
azoxystrobin	increases expression	1
CGP 52608	affects binding, increases reaction	1
deguelin	increases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
pyrimidifen	increases expression	1
ICG 001	decreases expression	1
bisphenol B	increases expression	1
pyrachlostrobin	increases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
bisphenol S	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
picoxystrobin	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1
Antimycin A	increases expression	1
Benzo(a)pyrene	increases expression	1
Copper	affects cotreatment, decreases expression, increases abundance	1

ChEMBL screening assays

90 unique, capped per target: 90 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1920845	Binding	Induction of ribosome to readthrough in human A-T lymphoblastoid cells assessed as ATM ser1981 autophosphorylation at 30 uM after 4 days by PTT-ELISA assay	Synthesis and evaluation of compounds that induce readthrough of premature termination codons. — Bioorg Med Chem Lett

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TJ58	HAP1 RPS25 (-) 1	Cancer cell line	Male
CVCL_TJ59	HAP1 RPS25 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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