RPL29

Summary

RPL29 (ribosomal protein L29, HGNC:10331) is a protein-coding gene on chromosome 3p21.2, encoding Large ribosomal subunit protein eL29 (P47914). Component of the large ribosomal subunit.

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 cytoplasmic ribosomal protein that is a component of the 60S subunit. The protein belongs to the L29E family of ribosomal proteins. The protein is also a peripheral membrane protein expressed on the cell surface that directly binds heparin. Although this gene was previously reported to map to 3q29-qter, it is believed that it is located at 3p21.3-p21.2. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome.

Source: NCBI Gene 6159 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_000992

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10331
Approved symbol	RPL29
Name	ribosomal protein L29
Location	3p21.2
Locus type	gene with protein product
Status	Approved
Aliases	HIP, HUMRPL29, L29, eL29
Ensembl gene	ENSG00000162244
Ensembl biotype	protein_coding
OMIM	601832
Entrez	6159

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000294189, ENST00000466397, ENST00000475248, ENST00000479017, ENST00000480306, ENST00000481629, ENST00000486565, ENST00000492277, ENST00000495383, ENST00000648640, ENST00000885407, ENST00000885408, ENST00000939894, ENST00000939895, ENST00000939896, ENST00000939897, ENST00000939898, ENST00000939899, ENST00000939900, ENST00000941354

RefSeq mRNA: 1 — MANE Select: NM_000992 NM_000992

CCDS: CCDS2845

Canonical transcript exons

ENST00000294189 — 4 exons

Exon	Start	End
ENSE00001081274	51995042	51995106
ENSE00001247981	51995425	51995469
ENSE00001889787	51995857	51995895
ENSE00003840482	51993522	51994126

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 99.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 232.4194 / max 1337.0827, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42392	226.4809	1823
42393	5.9384	1493

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	99.81	gold quality
zone of skin	UBERON:0000014	99.81	gold quality
skin of abdomen	UBERON:0001416	99.81	gold quality
skin of leg	UBERON:0001511	99.81	gold quality
left ovary	UBERON:0002119	99.81	gold quality
right uterine tube	UBERON:0001302	99.80	gold quality
right ovary	UBERON:0002118	99.80	gold quality
ganglionic eminence	UBERON:0004023	99.80	gold quality
cortical plate	UBERON:0005343	99.80	gold quality
embryo	UBERON:0000922	99.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	99.79	gold quality
right adrenal gland cortex	UBERON:0035827	99.79	gold quality
granulocyte	CL:0000094	99.78	gold quality
endocervix	UBERON:0000458	99.78	gold quality
adipose tissue	UBERON:0001013	99.78	gold quality
right adrenal gland	UBERON:0001233	99.78	gold quality
left adrenal gland	UBERON:0001234	99.78	gold quality
muscle of leg	UBERON:0001383	99.78	gold quality
gastrocnemius	UBERON:0001388	99.78	gold quality
mammary gland	UBERON:0001911	99.78	gold quality
subcutaneous adipose tissue	UBERON:0002190	99.78	gold quality
thoracic mammary gland	UBERON:0005200	99.78	gold quality
omental fat pad	UBERON:0010414	99.78	gold quality
ectocervix	UBERON:0012249	99.78	gold quality
left adrenal gland cortex	UBERON:0035825	99.78	gold quality
body of pancreas	UBERON:0001150	99.77	gold quality
muscle organ	UBERON:0001630	99.77	gold quality
fallopian tube	UBERON:0003889	99.77	gold quality
body of uterus	UBERON:0009853	99.77	gold quality
skeletal muscle organ	UBERON:0014892	99.77	gold quality

Single-cell (SCXA)

Detected in 36 experiment(s), a significant marker in 12.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	5128.48
E-CURD-122	yes	103.14
E-CURD-88	yes	63.70
E-MTAB-9221	yes	53.11
E-HCAD-11	yes	43.02
E-MTAB-9067	yes	28.22
E-MTAB-10042	yes	16.89
E-HCAD-9	yes	11.70
E-HCAD-35	yes	7.82
E-MTAB-9801	yes	6.08
E-GEOD-137537	yes	5.66
E-MTAB-10885	no	6251.59
E-HCAD-1	no	6182.15
E-MTAB-10287	no	6054.11
E-MTAB-11121	no	5741.68

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTNNB1

miRNA regulators (miRDB)

1 targeting RPL29, 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-LET-7C-3P	99.95	73.42	2862

Literature-anchored findings (GeneRIF, showing 9)

• HIP peptide-1 cannot recognize heparin via bio-specific interactions but binds glycosaminoglycans by non-specific charge interactions. (PMID:12659638)
• HIP is an islet protein naturally processed and presented by HLA-DR4 molecules (PMID:15721314)
• HIP/RPL29 plays a role in the cellular differentiation process in colon cancer cells. (PMID:16475173)
• Hip is a pro-survival substrate of granzyme B (PMID:17620340)
• HIP/RPL29 antagonizes VEGF and FGF2 stimulated angiogenesis by interfering with HS-dependent responses (PMID:18980226)
• Knockdown of L29 or L30 enhanced the interaction of MDM2 with L11 and L5 and markedly inhibited MDM2-mediated p53 ubiquitination, suggesting that direct perturbation of 60 S ribosomal biogenesis activates p53 via L11- and L5-mediated MDM2 suppression. (PMID:20554519)
• The results showed that knockdown of RPL26 or RPL29 expression significantly suppressed cell proliferation, induced cell arrest at G0/G1 phase and enhanced cell apoptosis (PMID:22868929)
• RPL29 is upregulated in the gingival squamous cell carcinoma.RPL29 role in the cell proliferation of the gingival squamous cell carcinoma. (PMID:31882427)
• The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data. (PMID:32798643)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	rpl29	ENSDARG00000077717
mus_musculus	Rpl29	ENSMUSG00000048758
mus_musculus	Rpl27rt	ENSMUSG00000078240
rattus_norvegicus	AABR07048253.1	ENSRNOG00000005694
rattus_norvegicus	Rpl29	ENSRNOG00000011138
rattus_norvegicus	LOC120093247	ENSRNOG00000029594
rattus_norvegicus	AABR07068694.1	ENSRNOG00000032822
rattus_norvegicus	AABR07043813.1	ENSRNOG00000033224
rattus_norvegicus	Rps29-ps20	ENSRNOG00000033695
rattus_norvegicus	AABR07058937.1	ENSRNOG00000036836
rattus_norvegicus	LOC120098629	ENSRNOG00000037172
rattus_norvegicus	LOC120095889	ENSRNOG00000050264
rattus_norvegicus		ENSRNOG00000085625
drosophila_melanogaster	RpL29	FBGN0016726
caenorhabditis_elegans		WBGENE00004443

Protein

Protein identifiers

Large ribosomal subunit protein eL29 — P47914 (reviewed: P47914)

Alternative names: 60S ribosomal protein L29, Cell surface heparin-binding protein HIP

All UniProt accessions (4): A0A3B3ITT5, C9IYI4, P47914, F8WF43

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Component of the large ribosomal subunit.

Subcellular location. Cytoplasm.

Similarity. Belongs to the eukaryotic ribosomal protein eL29 family.

RefSeq proteins (1): NP_000983* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002673	Ribosomal_eL29	Family

Pfam: PF01779

UniProt features (13 total): modified residue 4, compositionally biased region 3, sequence conflict 2, region of interest 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

172 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8A3D	ELECTRON MICROSCOPY	1.67
8GLP	ELECTRON MICROSCOPY	1.67
8QYX	ELECTRON MICROSCOPY	1.78
8QOI	ELECTRON MICROSCOPY	1.9
9O3W	ELECTRON MICROSCOPY	1.9
8YOO	ELECTRON MICROSCOPY	2
9C3H	ELECTRON MICROSCOPY	2
9I2D	ELECTRON MICROSCOPY	2.19
9PBE	ELECTRON MICROSCOPY	2.19
8QFD	ELECTRON MICROSCOPY	2.2
8YOP	ELECTRON MICROSCOPY	2.2
9GUL	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
7OW7	ELECTRON MICROSCOPY	2.4
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
8FLE	ELECTRON MICROSCOPY	2.48
9P8B	ELECTRON MICROSCOPY	2.48
7XNY	ELECTRON MICROSCOPY	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P47914-F1	82.49	0.60

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 (4): 142, 5, 31, 33

Function

Pathways and Gene Ontology

Reactome pathways

16 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-72689	Formation of a pool of free 40S subunits
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-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-9954709	Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide
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

MSigDB gene sets: 203 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, MODULE_151, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCM_NPM1, GOBP_STRIATED_MUSCLE_CELL_DIFFERENTIATION, HSIAO_HOUSEKEEPING_GENES, GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_TRANSLATION, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, GOBP_MUSCLE_CONTRACTION, GOBP_REGULATION_OF_SYNCYTIUM_FORMATION_BY_PLASMA_MEMBRANE_FUSION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, INGRAM_SHH_TARGETS_UP, SYED_ESTRADIOL_RESPONSE

GO Biological Process (3): cytoplasmic translation (GO:0002181), translation (GO:0006412), embryo implantation (GO:0007566)

GO Molecular Function (4): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), heparin binding (GO:0008201), cadherin binding (GO:0045296)

GO Cellular Component (7): cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), cytosolic large ribosomal subunit (GO:0022625), cytosolic ribosome (GO:0022626), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-11 pathways:

Category	Pathways
Ribosome-associated quality control	3
Translation	2
Cap-dependent Translation Initiation	2
Nonsense-Mediated Decay (NMD)	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
Signaling by ROBO receptors	1
Cellular response to starvation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
ribosome	2
translation	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
multicellular organism development	1
female pregnancy	1
reproductive process	1
nucleic acid binding	1
structural molecule activity	1
glycosaminoglycan binding	1
sulfur compound binding	1
cell adhesion molecule binding	1
intracellular anatomical structure	1
cytoplasm	1
large ribosomal subunit	1
cytosolic ribosome	1
cytosol	1
intracellular membraneless organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

2640 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RPL29	RPL35A	P18077	883
RPL29	RPL37A	P12751	879
RPL29	RPS25	P25111	829
RPL29	RPL14	P50914	784
RPL29	RPS2	P15880	769
RPL29	RPL5	P46777	758
RPL29	RPL4	P36578	754
RPL29	RPL6	Q02878	754
RPL29	RPL11	P25121	740
RPL29	RPS18	P25232	739
RPL29	RPL3	P39023	722
RPL29	RPL35	P42766	718
RPL29	RPL34	P49207	704
RPL29	RPL31	P12947	702
RPL29	RPS16	P17008	693

IntAct

152 interactions, top by confidence:

A	B	Type	Score
N	HNRNPR	psi-mi:“MI:0914”(association)	0.730
JADE1	KAT7	psi-mi:“MI:0914”(association)	0.720
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
RACK1	RPS17	psi-mi:“MI:0915”(physical association)	0.610
RPL29	HMGB1	psi-mi:“MI:0915”(physical association)	0.550
HMGB1	RPL29	psi-mi:“MI:0915”(physical association)	0.550
MECP2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPL37A	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
CUEDC2	TBP	psi-mi:“MI:0914”(association)	0.530
DDX6	MCRIP1	psi-mi:“MI:0914”(association)	0.510
UBE3A	HERC2	psi-mi:“MI:0914”(association)	0.500
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
CFTR	CNOT1	psi-mi:“MI:0914”(association)	0.480
ESR1		psi-mi:“MI:0914”(association)	0.460
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
FUS	DDX3X	psi-mi:“MI:0914”(association)	0.430
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
RPL29	RPL7	psi-mi:“MI:0915”(physical association)	0.400
RPL29	DDX18	psi-mi:“MI:0915”(physical association)	0.400
	GNAT3	psi-mi:“MI:0915”(physical association)	0.400
YWHAE	HNRNPA1	psi-mi:“MI:0915”(physical association)	0.400
C1QBP	RPS3	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (388): RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Co-fractionation), RPL29 (Co-fractionation), RPL29 (Co-fractionation), RPL9 (Co-fractionation), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Proximity Label-MS), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS), RPL29 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D8PF57, A4G029, A6VIE9, A7HBM2, A9A8D5, B4UBA3, B8J864, C1CXG2, C5A7H4, C6A264, O28212, O59931, O96269, P05733, P05747, P0DJ21, P22452, P25886, P47914, P47915, P54573, P61927, P61928, P79244, Q24154, Q2IJ80, Q54MG6, Q54TW3, Q58DW3, Q5JGT6, Q605B6, Q6BPF6, Q6CW22, Q6F482, Q6M0V9, Q6MJ18, Q72NG5, Q758D8, Q84WM0, Q8HXB8

Diamond homologs: A0A1D8PF57, G1SGR6, P05747, P0DJ21, P25886, P47914, P47915, Q24154, Q54TW3, Q58DW3, Q84WM0, Q8HXB8, Q92366, Q95281, Q9M7X7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
RPL29	“form complex”	“60S cytosolic large ribosomal subunit”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 170 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
Nuclear events stimulated by ALK signaling in cancer	6	15.5×	9e-05
SARS-CoV-1 modulates host translation machinery	6	14.7×	1e-04
Eukaryotic Translation Initiation	5	12.2×	1e-03
Cap-dependent Translation Initiation	5	12.2×	1e-03
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	12	11.2×	2e-07
SARS-CoV-1-host interactions	8	11.2×	3e-05
SRP-dependent cotranslational protein targeting to membrane	14	11.1×	2e-08
Peptide chain elongation	11	11.1×	4e-07

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of mRNA splicing, via spliceosome	5	25.0×	4e-04
stress granule assembly	5	19.7×	8e-04
cytoplasmic translation	13	15.7×	2e-09
mRNA stabilization	6	14.4×	8e-04
negative regulation of translation	9	11.5×	3e-05
translation	13	8.7×	2e-06
rRNA processing	8	7.4×	2e-03
mRNA splicing, via spliceosome	10	6.0×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

371 predictions. Top by Δscore:

Variant	Effect	Δscore
3:51994122:TCCAC:T	acceptor_gain	1.0000
3:51994123:CCAC:C	acceptor_gain	1.0000
3:51994123:CCACC:C	acceptor_gain	1.0000
3:51994124:CAC:C	acceptor_gain	1.0000
3:51994124:CACC:C	acceptor_gain	1.0000
3:51994125:AC:A	acceptor_gain	1.0000
3:51994126:CC:C	acceptor_gain	1.0000
3:51994126:CCT:C	acceptor_loss	1.0000
3:51994127:C:CC	acceptor_gain	1.0000
3:51994127:CTG:C	acceptor_loss	1.0000
3:51994135:C:CT	acceptor_gain	1.0000
3:51994136:A:T	acceptor_gain	1.0000
3:51995036:ACTC:A	donor_loss	1.0000
3:51995037:CT:C	donor_loss	1.0000
3:51995038:T:TA	donor_loss	1.0000
3:51995039:CACC:C	donor_loss	1.0000
3:51995040:A:T	donor_loss	1.0000
3:51995040:AC:A	donor_gain	1.0000
3:51995040:ACC:A	donor_gain	1.0000
3:51995040:ACCC:A	donor_gain	1.0000
3:51995040:ACCCC:A	donor_gain	1.0000
3:51995041:C:CA	donor_loss	1.0000
3:51995041:CC:C	donor_gain	1.0000
3:51995041:CCC:C	donor_gain	1.0000
3:51995041:CCCC:C	donor_gain	1.0000
3:51995041:CCCCC:C	donor_gain	1.0000
3:51995060:T:C	donor_gain	1.0000
3:51995103:CGGG:C	acceptor_gain	1.0000
3:51995104:GGG:G	acceptor_gain	1.0000
3:51995104:GGGC:G	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000729098 (3:51997099 A>C), RS1001394559 (3:51997094 G>C), RS1001988804 (3:51993192 C>T), RS1002217181 (3:51997622 T>A,C), RS1003495295 (3:51995176 C>T), RS1003746352 (3:51994810 T>G), RS1004056205 (3:51997514 T>C), RS1004427743 (3:51997669 T>G), RS1005488545 (3:51995965 C>A,T), RS1005588611 (3:51994821 G>A), RS1005792266 (3:51993153 G>A,C), RS1006520664 (3:51995847 C>G,T), RS1007543289 (3:51994432 G>C), RS1008240317 (3:51997139 G>T), RS1009552744 (3:51995623 C>T)

Disease associations

OMIM: gene MIM:601832 | 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 (1): CHEMBL3987582 (PROTEIN NUCLEIC-ACID COMPLEX)

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

46 potent at pChembl≥5 of 50 total, top 45 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
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
5.55	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

46 with measured affinity, of 205 total; 26 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
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
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

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

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	decreases expression, increases abundance, increases expression	4
bisphenol A	decreases expression, increases expression	3
titanium dioxide	increases expression	2
sodium arsenite	decreases expression	2
chloropicrin	affects expression, decreases expression	2
bisphenol S	increases expression	2
bisphenol AF	increases expression	2
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases oxidation	2
Caffeine	decreases phosphorylation, increases expression	2
Tunicamycin	decreases expression	2
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
arsenite	affects binding, increases reaction	1
perfluorooctanoic acid	increases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
epigallocatechin gallate	increases expression	1
perfluorooctane sulfonic acid	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
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
jinfukang	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, decreases expression, increases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1

ChEMBL screening assays

89 unique, capped per target: 89 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

Clinical trials (associated diseases)

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