LTN1

Summary

LTN1 (listerin E3 ubiquitin protein ligase 1, HGNC:13082) is a protein-coding gene on chromosome 21q21.3, encoding E3 ubiquitin-protein ligase listerin (O94822). E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation.

Like most RING finger proteins, LTN1 functions as an E3 ubiquitin ligase (Chu et al., 2009 [PubMed 19196968]).

Source: NCBI Gene 26046 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 244 total
• Druggable target: yes
• MANE Select transcript: NM_015565

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13082
Approved symbol	LTN1
Name	listerin E3 ubiquitin protein ligase 1
Location	21q21.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0714, FLJ11053, LISTERIN
Ensembl gene	ENSG00000198862
Ensembl biotype	protein_coding
OMIM	613083
Entrez	26046

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000361371, ENST00000389194, ENST00000389195, ENST00000475344, ENST00000483326, ENST00000486427, ENST00000614971, ENST00000881243, ENST00000912877, ENST00000912878, ENST00000912879

RefSeq mRNA: 2 — MANE Select: NM_015565 NM_001320766, NM_015565

CCDS: CCDS33527

Canonical transcript exons

ENST00000361371 — 30 exons

Exon	Start	End
ENSE00001436303	28992764	28992877
ENSE00001505143	28986731	28986934
ENSE00001621538	28947464	28947606
ENSE00001622947	28960517	28960706
ENSE00001642510	28952160	28952264
ENSE00001650919	28935109	28935329
ENSE00001657296	28944383	28944596
ENSE00001666120	28943667	28943904
ENSE00001681558	28956762	28956948
ENSE00001682761	28936526	28936697
ENSE00001688591	28928144	28930510
ENSE00001703316	28941220	28941406
ENSE00001705186	28959458	28959697
ENSE00001713856	28945807	28945951
ENSE00001718587	28965865	28965906
ENSE00001729415	28957332	28957476
ENSE00001732602	28931155	28931322
ENSE00001735330	28932470	28932664
ENSE00001741886	28943262	28943336
ENSE00001748537	28958386	28958539
ENSE00001750264	28946152	28946287
ENSE00001766793	28953217	28953376
ENSE00002722595	28966370	28967179
ENSE00003496895	28982316	28982368
ENSE00003523511	28986139	28986237
ENSE00003583906	28970552	28970742
ENSE00003589298	28984692	28984922
ENSE00003633682	28969466	28969601
ENSE00003637644	28981119	28981299
ENSE00003680289	28971271	28971444

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 96.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.4845 / max 520.5188, expressed in 1805 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
190060	24.1683	1804
190061	0.2123	57
190059	0.0776	26
209292	0.0262	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	96.52	gold quality
decidua	UBERON:0002450	94.77	gold quality
biceps brachii	UBERON:0001507	94.34	gold quality
endothelial cell	CL:0000115	94.15	gold quality
oocyte	CL:0000023	93.91	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.74	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.57	gold quality
upper leg skin	UBERON:0004262	93.42	gold quality
skin of hip	UBERON:0001554	93.33	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	93.18	gold quality
cauda epididymis	UBERON:0004360	92.76	gold quality
heart right ventricle	UBERON:0002080	92.71	gold quality
colonic mucosa	UBERON:0000317	92.59	gold quality
jejunal mucosa	UBERON:0000399	92.46	gold quality
buccal mucosa cell	CL:0002336	92.42	gold quality
corpus epididymis	UBERON:0004359	92.25	gold quality
calcaneal tendon	UBERON:0003701	91.96	gold quality
seminal vesicle	UBERON:0000998	91.84	gold quality
choroid plexus epithelium	UBERON:0003911	91.81	gold quality
caput epididymis	UBERON:0004358	91.62	gold quality
jejunum	UBERON:0002115	91.26	gold quality
oral cavity	UBERON:0000167	91.08	gold quality
tibia	UBERON:0000979	91.00	gold quality
blood vessel layer	UBERON:0004797	90.95	gold quality
cartilage tissue	UBERON:0002418	90.81	gold quality
corpus callosum	UBERON:0002336	90.54	gold quality
superficial temporal artery	UBERON:0001614	90.45	gold quality
trabecular bone tissue	UBERON:0002483	90.42	gold quality
parotid gland	UBERON:0001831	90.40	gold quality
postcentral gyrus	UBERON:0002581	90.36	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.89
E-CURD-10	no	327.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting LTN1, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1468-3P	99.96	72.74	3797

Literature-anchored findings (GeneRIF, showing 4)

• Results show that Listerin specificity for nascent chain-60S complexes depends on nuclear export mediator factor. (PMID:25578875)
• E3 ligase listerin accesses nascent polypeptides stalled at the Sec61 translocon via a gap in the ribosome-translocon junction near the Sec61 lateral gate. (PMID:25877867)
• Expression Analysis of Ermin and Listerin E3 Ubiquitin Protein Ligase 1 Genes in the Periphery of Patients with Schizophrenia. (PMID:34676516)
• LTN1 promotes RLR degradation to inhibit immune response to RNA virus through the ESCRT pathway. (PMID:38060409)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ltn1	ENSDARG00000003984
mus_musculus	Ltn1	ENSMUSG00000052299
rattus_norvegicus	Ltn1	ENSRNOG00000001602
drosophila_melanogaster	Ltn1	FBGN0262517
caenorhabditis_elegans	Y54E10A.11	WBGENE00021831

Protein

Protein identifiers

E3 ubiquitin-protein ligase listerin — O94822 (reviewed: O94822)

Alternative names: RING finger protein 160, RING-type E3 ubiquitin transferase listerin, Zinc finger protein 294

All UniProt accessions (3): O94822, H7BYG8, S4R3T2

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. Within the RQC complex, LTN1 is recruited to stalled 60S ribosomal subunits by NEMF and mediates ubiquitination of stalled nascent chains. Ubiquitination leads to VCP/p97 recruitment for extraction and degradation of the incomplete translation product.

Subunit / interactions. Component of the ribosome quality control complex (RQC), composed of the E3 ubiquitin ligase LTN1, TCF25 and NEMF associated with the 60S ribosomal subunit. The complex probably also contains VCP/p97 and its ubiquitin-binding cofactors.

Subcellular location. Cytoplasm. Cytosol.

Post-translational modifications. Autoubiquitinated.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the LTN1 family.

Isoforms (3)

UniProt ID	Names	Canonical?
O94822-1	1	yes
O94822-2	2
O94822-3	3

RefSeq proteins (2): NP_001307695, NP_056380* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001841	Znf_RING	Domain
IPR011016	Znf_RING-CH	Domain
IPR011989	ARM-like	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR039795	LTN1/Rkr1	Family
IPR039804	RING-CH-C4HC3_LTN1	Domain
IPR054476	Ltn1_N	Domain
IPR054477	LTN1_E3_ligase_6th	Domain
IPR054478	LTN1_UBC	Domain
IPR056241	LTN1_HEAT_5th	Domain

Pfam: PF22958, PF22999, PF23009, PF24618

UniProt features (31 total): repeat 16, sequence conflict 7, sequence variant 4, splice variant 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
9GY4	ELECTRON MICROSCOPY	3
3J92	ELECTRON MICROSCOPY	3.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O94822-F1	80.79	0.33

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-9954709	Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide
R-HSA-1280218	Adaptive Immune System
R-HSA-168256	Immune System
R-HSA-983169	Class I MHC mediated antigen processing & presentation

MSigDB gene sets: 164 (showing top): ACTACCT_MIR196A_MIR196B, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, MORF_ATRX, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, TGACCTY_ERR1_Q2, GOBP_TRANSLATION, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_PROTEIN_AUTOUBIQUITINATION, ATTACAT_MIR3803P, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_TRANSLATIONAL_ELONGATION, GOBP_PROTEASOMAL_PROTEIN_CATABOLIC_PROCESS, CTTTGTA_MIR524

GO Biological Process (5): protein autoubiquitination (GO:0051865), rescue of stalled cytosolic ribosome (GO:0072344), ribosome-associated ubiquitin-dependent protein catabolic process (GO:1990116), protein ubiquitination (GO:0016567), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)

GO Molecular Function (7): zinc ion binding (GO:0008270), ribosomal large subunit binding (GO:0043023), ubiquitin protein ligase activity (GO:0061630), ubiquitin-protein transferase activity (GO:0004842), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (4): cytosol (GO:0005829), cytosolic ribosome (GO:0022626), RQC complex (GO:1990112), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Class I MHC mediated antigen processing & presentation	1
Ribosome-associated quality control	1
Immune System	1
Adaptive Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
protein ubiquitination	1
cytoplasmic translational elongation	1
ribosome disassembly	1
proteasome-mediated ubiquitin-dependent protein catabolic process	1
protein modification by small protein conjugation	1
ubiquitin-dependent protein catabolic process	1
proteasomal protein catabolic process	1
transition metal ion binding	1
ribosome binding	1
ubiquitin-protein transferase activity	1
ubiquitin-like protein ligase activity	1
ubiquitin-like protein transferase activity	1
binding	1
catalytic activity	1
cation binding	1
cytoplasm	1
cytosol	1
ribosome	1
protein-containing complex	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1706 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LTN1	NEMF	O60524	968
LTN1	VCP	P55072	904
LTN1	ANKZF1	Q9H8Y5	862
LTN1	TCF25	Q9BQ70	841
LTN1	ZNF598	Q86UK7	815
LTN1	HBS1L	Q9Y450	796
LTN1	UBE2A	P49459	767
LTN1	ABCE1	P61221	762
LTN1	CNOT4	O95628	744
LTN1	UFD1	Q92890	702
LTN1	UBR1	Q8IWV7	687
LTN1	NPLOC4	Q8TAT6	679
LTN1	UBA1	P22314	646
LTN1	PELO	Q9BRX2	643
LTN1	MARCHF6	O60337	576

IntAct

152 interactions, top by confidence:

A	B	Type	Score
TIRAP	TLR4	psi-mi:“MI:0914”(association)	0.810
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
LAMP3	METTL15	psi-mi:“MI:0914”(association)	0.530
NPY2R	RTL8C	psi-mi:“MI:0914”(association)	0.530
EPHA1	EXOC5	psi-mi:“MI:0914”(association)	0.530
VASN	AP3B1	psi-mi:“MI:0914”(association)	0.530
EGFR	NDUFA4	psi-mi:“MI:0914”(association)	0.530
ARRDC4	WWP2	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
TGOLN2	DENND11	psi-mi:“MI:0914”(association)	0.530
CD226	MEN1	psi-mi:“MI:0914”(association)	0.530
RNF19B	PIK3R2	psi-mi:“MI:0914”(association)	0.530
CA14	EXOC5	psi-mi:“MI:0914”(association)	0.530
CHRM3	PLD2	psi-mi:“MI:0914”(association)	0.530
HLA-B	LTN1	psi-mi:“MI:0914”(association)	0.530
B3GALT2	LTN1	psi-mi:“MI:0914”(association)	0.530
ILVBL	SLC33A1	psi-mi:“MI:0914”(association)	0.530
IRF7	AIP	psi-mi:“MI:0914”(association)	0.500
LTN1	TIRAP	psi-mi:“MI:0915”(physical association)	0.500
LTN1	STING1	psi-mi:“MI:0915”(physical association)	0.500
LTN1	IRF7	psi-mi:“MI:0915”(physical association)	0.500

BioGRID (301): NEMF (Co-fractionation), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Affinity Capture-MS), LTN1 (Co-fractionation), LTN1 (Co-fractionation), LTN1 (Co-fractionation), LTN1 (Affinity Capture-MS), DHCR7 (Affinity Capture-MS)

ESM2 similar proteins: A0JM49, A2AKG8, B0V0U5, B1AUR6, C5J7W8, E1BGH8, E1C231, E1C2Z0, E7FGT5, E7FH61, E9Q3L2, F6S215, O08662, O60287, O94822, P42356, P57678, P78527, P97313, Q13315, Q13535, Q14146, Q1RLU1, Q2TAW0, Q3TQQ9, Q3URQ0, Q571H0, Q5RDK1, Q5VW36, Q5WNI9, Q5XI94, Q5ZM41, Q62388, Q6A009, Q6DFV1, Q6PQD5, Q6ZRQ5, Q7SY48, Q86XI2, Q8BKX6

Diamond homologs: A0JM49, B6IFN4, E1C231, O74349, O94822, Q04781, Q555H8, Q65XX2, Q6A009, Q9FGI1, Q7S834, Q9VW09

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
Ub:E2	“up-regulates activity”	LTN1	ubiquitination
LTN1	“down-regulates activity”	RPS6KA1	ubiquitination
LTN1	“form complex”	“RQC complex”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	202
Likely benign	15
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

5065 predictions. Top by Δscore:

Variant	Effect	Δscore
21:28930506:TTGTA:T	acceptor_gain	1.0000
21:28930507:TGTA:T	acceptor_gain	1.0000
21:28930508:GTA:G	acceptor_gain	1.0000
21:28930509:TA:T	acceptor_gain	1.0000
21:28930511:C:CC	acceptor_gain	1.0000
21:28931319:CATT:C	acceptor_gain	1.0000
21:28931321:TT:T	acceptor_gain	1.0000
21:28931323:C:CC	acceptor_gain	1.0000
21:28931324:T:C	acceptor_loss	1.0000
21:28932661:TAAC:T	acceptor_gain	1.0000
21:28932662:AACC:A	acceptor_loss	1.0000
21:28932665:C:CC	acceptor_gain	1.0000
21:28932666:T:A	acceptor_loss	1.0000
21:28936520:A:AC	donor_gain	1.0000
21:28936521:C:CC	donor_gain	1.0000
21:28943260:A:AC	donor_gain	1.0000
21:28943261:C:CC	donor_gain	1.0000
21:28943261:CAAGG:C	donor_gain	1.0000
21:28943665:A:AC	donor_gain	1.0000
21:28943666:C:CC	donor_gain	1.0000
21:28943789:T:C	donor_gain	1.0000
21:28944443:T:A	donor_gain	1.0000
21:28944450:A:AC	donor_gain	1.0000
21:28944451:C:CC	donor_gain	1.0000
21:28946147:CCTA:C	donor_loss	1.0000
21:28946148:CTAC:C	donor_loss	1.0000
21:28946150:A:AC	donor_gain	1.0000
21:28946151:C:A	donor_loss	1.0000
21:28946151:C:CC	donor_gain	1.0000
21:28946151:CCAA:C	donor_gain	1.0000

AlphaMissense

11628 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
21:28930466:A:C	C1761W	1.000
21:28930467:C:G	C1761S	1.000
21:28930467:C:T	C1761Y	1.000
21:28930468:A:G	C1761R	1.000
21:28930468:A:T	C1761S	1.000
21:28930475:A:C	C1758W	1.000
21:28930476:C:G	C1758S	1.000
21:28930476:C:T	C1758Y	1.000
21:28930477:A:G	C1758R	1.000
21:28930477:A:T	C1758S	1.000
21:28930499:A:C	F1750L	1.000
21:28930499:A:T	F1750L	1.000
21:28930500:A:G	F1750S	1.000
21:28930501:A:G	F1750L	1.000
21:28930502:C:A	W1749C	1.000
21:28930502:C:G	W1749C	1.000
21:28930504:A:G	W1749R	1.000
21:28930504:A:T	W1749R	1.000
21:28931156:A:G	L1746S	1.000
21:28931158:G:C	C1745W	1.000
21:28931159:C:G	C1745S	1.000
21:28931159:C:T	C1745Y	1.000
21:28931160:A:G	C1745R	1.000
21:28931160:A:T	C1745S	1.000
21:28931167:A:C	H1742Q	1.000
21:28931167:A:T	H1742Q	1.000
21:28931169:G:C	H1742D	1.000
21:28931169:G:T	H1742N	1.000
21:28931170:G:C	F1741L	1.000
21:28931170:G:T	F1741L	1.000

dbSNP variants (sampled 300 via entrez): RS1000136079 (21:28965073 G>A), RS1000171676 (21:28968164 C>A,T), RS1000273739 (21:28964830 C>G,T), RS1000282944 (21:28962505 G>A), RS1000372099 (21:28955193 G>A,C), RS1000426753 (21:28958899 A>AG), RS1000454190 (21:28993829 C>G), RS1000484633 (21:28927824 C>T), RS1000587547 (21:28950674 C>T), RS1000589731 (21:28941281 A>C), RS1000606100 (21:28963273 G>C), RS1000650670 (21:28971818 C>T), RS1000750843 (21:28933496 C>T), RS1000803896 (21:28994233 C>T), RS1000831243 (21:28955611 G>A)

Disease associations

OMIM: gene MIM:613083 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST004612_187	High light scatter reticulocyte percentage of red cells	3.000000e-09
GCST004619_186	Reticulocyte fraction of red cells	5.000000e-09
GCST005026_10	Initial pursuit acceleration in psychotic disorders	8.000000e-08
GCST008162_70	Hip circumference	9.000000e-07
GCST009391_1693	Metabolite levels	6.000000e-07
GCST90002385_571	High light scatter reticulocyte count	3.000000e-31
GCST90002386_526	High light scatter reticulocyte percentage of red cells	3.000000e-33
GCST90002387_172	Immature fraction of reticulocytes	8.000000e-19
GCST90002405_410	Reticulocyte count	4.000000e-25
GCST90002406_563	Reticulocyte fraction of red cells	2.000000e-27

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count
EFO:0008434	initial pursuit acceleration
EFO:0010344	cholesteryl ester 18:1 measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066997 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 4 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.12	Kd	753.4	nM	CHEMBL5653589
6.12	ED50	753.4	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 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
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148674: Binding affinity to human LTN1 incubated for 45 mins by Kinobead based pull down assay	kd	0.7534	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, decreases expression, increases expression, affects cotreatment	3
trichostatin A	affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, increases expression	3
Cisplatin	affects cotreatment, decreases expression	2
Valproic Acid	decreases expression	2
aristolochic acid I	decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
chloroacetaldehyde	decreases expression	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
myricetin	decreases expression	1
beta-methylcholine	affects expression	1
celastrol	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
gedunin	decreases expression	1
2-palmitoylglycerol	increases expression	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, decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression, affects cotreatment	1
Rosiglitazone	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651716	Binding	Binding affinity to human LTN1 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D8PJ	Ubigene HCT 116 LTN1 KO	Cancer cell line	Male
CVCL_E0GS	Ubigene HeLa LTN1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice