MAP1LC3B

Summary

MAP1LC3B (microtubule associated protein 1 light chain 3 beta, HGNC:13352) is a protein-coding gene on chromosome 16q24.2, encoding Microtubule-associated protein 1 light chain 3 beta (Q9GZQ8). Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes). It is a selective cancer dependency (DepMap: 12.6% of cell lines).

The product of this gene is a subunit of neuronal microtubule-associated MAP1A and MAP1B proteins, which are involved in microtubule assembly and important for neurogenesis. Studies on the rat homolog implicate a role for this gene in autophagy, a process that involves the bulk degradation of cytoplasmic component.

Source: NCBI Gene 81631 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 29 total
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 12.6% of screened cell lines
• MANE Select transcript: NM_022818

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13352
Approved symbol	MAP1LC3B
Name	microtubule associated protein 1 light chain 3 beta
Location	16q24.2
Locus type	gene with protein product
Status	Approved
Aliases	ATG8F
Ensembl gene	ENSG00000140941
Ensembl biotype	protein_coding
OMIM	609604
Entrez	81631

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000268607, ENST00000564638, ENST00000564844, ENST00000565788, ENST00000570189, ENST00000650688, ENST00000880068, ENST00000936306, ENST00000960545

RefSeq mRNA: 1 — MANE Select: NM_022818 NM_022818

CCDS: CCDS10960

Canonical transcript exons

ENST00000268607 — 4 exons

Exon	Start	End
ENSE00001317431	87392336	87392467
ENSE00003493083	87402175	87402281
ENSE00003495891	87398815	87398870
ENSE00003891741	87402923	87404774

Expression profiles

Bgee: expression breadth ubiquitous, 301 present calls, max score 98.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 142.5729 / max 1047.9171, expressed in 1828 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155477	140.6740	1828
155476	1.4276	828
155473	0.2079	86
155475	0.2010	20
155474	0.0624	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
paraflocculus	UBERON:0005351	98.86	gold quality
substantia nigra pars compacta	UBERON:0001965	98.76	gold quality
Brodmann (1909) area 10	UBERON:0013541	98.65	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.62	gold quality
adult organism	UBERON:0007023	98.61	gold quality
lateral nuclear group of thalamus	UBERON:0002736	98.55	gold quality
cerebellar hemisphere	UBERON:0002245	98.48	gold quality
cerebellar cortex	UBERON:0002129	98.42	gold quality
cerebellum	UBERON:0002037	98.39	gold quality
frontal pole	UBERON:0002795	98.28	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.26	gold quality
postcentral gyrus	UBERON:0002581	98.22	gold quality
lateral globus pallidus	UBERON:0002476	98.18	gold quality
pons	UBERON:0000988	98.17	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.16	gold quality
middle frontal gyrus	UBERON:0002702	98.15	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.14	gold quality
type B pancreatic cell	CL:0000169	98.10	gold quality
spinal cord	UBERON:0002240	98.10	gold quality
endometrium epithelium	UBERON:0004811	98.10	gold quality
cingulate cortex	UBERON:0003027	98.06	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.05	gold quality
hypothalamus	UBERON:0001898	98.04	gold quality
anterior cingulate cortex	UBERON:0009835	98.04	gold quality
prefrontal cortex	UBERON:0000451	97.99	gold quality
gastrocnemius	UBERON:0001388	97.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.94	gold quality
biceps brachii	UBERON:0001507	97.84	gold quality
diaphragm	UBERON:0001103	97.73	gold quality
dorsal root ganglion	UBERON:0000044	97.71	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-GEOD-111727	yes	626.31
E-MTAB-10287	yes	35.50
E-MTAB-9221	yes	12.60
E-MTAB-9067	yes	10.84
E-CURD-114	yes	10.49
E-HCAD-9	yes	5.57
E-CURD-122	yes	5.08
E-MTAB-6379	no	1841.37
E-MTAB-9154	no	1702.23
E-MTAB-8060	no	1206.54
E-MTAB-7303	no	379.07
E-ENAD-17	no	199.93
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ATF1, ATF3, ATF4, CEBPB, DDIT3, E2F1, ESR1, GDNF, STAT1, TFDP3

miRNA regulators (miRDB)

82 targeting MAP1LC3B, 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-5692A	100.00	74.40	6850
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-433-3P	99.98	69.37	1203
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-202-5P	99.78	67.65	991
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p (PMID:11825910)
• the essential site for the distinct post-translation modification of microtubule-associated protein 1 light chain 3B is Lys-122 rather than the conserved Gly-120 (PMID:12740394)
• Results indicate that the carboxyl terminus of MAP1LC3B is cleaved to expose Gly(120) for further ubiquitylation-like reactions. (PMID:15355958)
• The positive rates of Beclin1 and MAPLC3 were significantly lower in non-small cell lung cancer tissues than in adjacent non-cancerous tissues and normal tissues. (PMID:18184459)
• A large number of MAP1LC3A and MAP1LC3B positive breast cancer tissues cores have high proportion of stained cells (81-100%) as compared with normal breast tissues. (PMID:19623642)
• The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5. (PMID:20038797)
• The progression of astrocytic tumors was related to a decrease in autophagic capacity represented by the loss of LC3B-II and Beclin 1 expression (PMID:20863706)
• The results suggest that autophagic protein LC3B exerts a protective function during the pathogenesis of pulmonary hypertension (PMID:20889906)
• In solid tumors, high LC3B expression was associated proliferation, invasion and metastasis, high nuclear grade, and worse outcome. (PMID:22080440)
• The interaction of LC3B and Fas pathways requires cav-1.LC3B plays a regulatory role in hyperoxia-induced epithelial apoptosis (PMID:22095627)
• These data relate LC3B, ATG5 and ATG12 to mitochondrial quality control after oxidative damage, and to cellular longevity. (PMID:22170153)
• Data show that TFDP3 upregulates the expression of autophagy gene LC3B and inhibits E2F1-induced apoptosis, and may play an important role in prostate cancer. (PMID:22482402)
• Data show that VPRBP (viral protein R-binding protein)-LC3B (light-chain 3B)/p62(SQSTM1) were in the same protein complex. (PMID:22963397)
• positive fibroblastic LC3B correlates with lower invasion, and low expression of fibroblastic Cav-1 is a novel predictor of poor GC prognosis. (PMID:23203033)
• These preliminary results demonstrated that high LC3B expression was associated with lymph node and distant metastasis in triple-negative breast cancer (PMID:23371253)
• Data suggest that activated autophagy is associated with the progression of pancreatic ductal adenocarcinoma and that the overexpression of autophagy-related proteins Atg5, Ambra1, beclin-1, LC3B and Bif-1 is significantly correlated with poor outcome. (PMID:23429496)
• Data indicate that high cytoplasmic microtubule-associated protein 1 light chain LC3A, LC3B, Beclin 1 and p62/SQSTM1 expressions were independently linked with the Gleason score. (PMID:23787295)
• NMR and crystal structures of the autophagy modifier LC3B in complex with the LC3 interaction region of optineurin. (PMID:23805866)
• Beclin-1 and LC3-II are downregulated in hypopharyngeal squamous cell carcinoma patients, and their aberrant expression correlates with poor prognosis. (PMID:23935917)
• elevating the levels of TSC1 (tuberous sclerosis complex) and TSC2 and inactivating MTOR and RPS6KB/p70S6K, causing cleaved MAP1LC3B levels to increase (PMID:24113030)
• LC3B can be used as a prognostic marker in patients with non-pCR after NCT for breast cancer, which highlights the importance of autophagy in the biologic behavior of chemoresistant cancer cells (PMID:24141623)
• these data indicated that LC3B-II deacetylation, which was partly mediated by HDAC6, is involved in autophagic degradation during serum starvation. (PMID:24220335)
• The results of this study identify a new physiological role for the PSF-LC3B axis as a potential endogenous modulator of colon cancer treatment. (PMID:24288667)
• knockdown of LC3B but not GABARAPs resulted in significant accumulation of p62/Sqstm1, one of the selective substrates for autophagy (PMID:24582747)
• When not bound to autophagosomes, LC3B associates with a multicomponent complex with an effective size of ~500 kDa in the cytoplasm. (PMID:24646892)
• investigated the expression of autophagy-related markers microtubule-associated protein IA/IB light chain 3 (LC3) and p62/sequestosome-1 (p62), in cutaneous squamous cell carcinoma specimens and assessed their correlation to clinicopathological factors (PMID:24690104)
• High intensity of LC3B staining was predictive of poor prognosis. (PMID:24900981)
• High cytoplasmic p62 expression accompanied with either a low or high LC3B expression. (PMID:24983366)
• high expression of LC3B, correlated with vascular invasion and lymph node metastasis, might be a novel prognostic biomarker and would be a potential therapy target for HCC. (PMID:25256671)
• Data show that interaction between promyelocytic leukemia protein (PML) and microtubule-associated protein light chain 3 (LC3) contributes to cell growth inhibition function of PML. (PMID:25419843)
• This study unveils that HIV-1 Vif inhibits autophagy via interaction with LC3B independently of its action on APOBEC3G and, therefore, suggest a new function of this viral protein in restricting innate antiviral mechanisms. (PMID:25490467)
• mRNA levels of MAP1LC3B, an autophagic marker, showed a 5-fold decrease in symptomatic samples. (PMID:25503069)
• LC3B may promote the migration and invasion of EOC cells by affecting the cytoskeleton via the RhoA pathway. (PMID:25607473)
• FYCO1 requires a functional LC3A/B-preferring LC3-interacting Region (LIR) motif to facilitate efficient maturation of autophagosomes under basal conditions, whereas starvation-induced autophagy was unaffected (PMID:26468287)
• Data show CGK733 induced microtubule associated protein LC3B formation upstream of AMP-activated protein kinase and protein kinase RNA-like endoplasmic reticulum kinase/CCAAT-enhancer-binding protein homologous protein pathways and p21 Cip1 expression. (PMID:26486079)
• In microsatellite stable carcinomas, the level of LC3B-II expression was higher than that in the microsatellite unstable carcinomas. (PMID:26502823)
• the combined positivity for LC3B(+) puncta and nuclear HMGB1 is a positive predictor for longer BC survival (PMID:26506894)
• BAG3 maintains the basal amount of LC3B protein by controlling the translation of its mRNA in HeLa and HEK293 cells. (PMID:26654586)
• Loss of HPS1 protein results in impaired autophagy that is restored by exogenous LC3B and that defective autophagy might therefore play a critical role in the development and progression of Hermansky-Pudlak syndrome. (PMID:26719147)
• Collectively, our findings indicate that MIR494 reduces cell survival in 769-P renal cancer cells which is accompanied by increased lipid droplet formation (which occurs in a LC3B-dependent manner) and mitochondrial changes. (PMID:26794413)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	map1lc3b	ENSDARG00000101127
caenorhabditis_elegans		WBGENE00002981

Paralogs (6): GABARAPL2 (ENSG00000034713), MAP1LC3A (ENSG00000101460), GABARAPL1 (ENSG00000139112), GABARAP (ENSG00000170296), MAP1LC3C (ENSG00000197769), MAP1LC3B2 (ENSG00000258102)

Protein

Protein identifiers

Microtubule-associated protein 1 light chain 3 beta — Q9GZQ8 (reviewed: Q9GZQ8)

Alternative names: Autophagy-related protein LC3 B, Autophagy-related ubiquitin-like modifier LC3 B, MAP1 light chain 3-like protein 2, Microtubule-associated proteins 1A/1B light chain 3B

All UniProt accessions (6): Q9GZQ8, H3BM99, H3BTE7, H3BTL1, H6UMI0, Q658J6

UniProt curated annotations — full annotation on UniProt →

Function. Ubiquitin-like modifier involved in formation of autophagosomal vacuoles (autophagosomes). Plays a role in mitophagy which contributes to regulate mitochondrial quantity and quality by eliminating the mitochondria to a basal level to fulfill cellular energy requirements and preventing excess ROS production. In response to cellular stress and upon mitochondria fission, binds C-18 ceramides and anchors autophagolysosomes to outer mitochondrial membranes to eliminate damaged mitochondria. While LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation. Promotes primary ciliogenesis by removing OFD1 from centriolar satellites via the autophagic pathway. Through its interaction with the reticulophagy receptor TEX264, participates in the remodeling of subdomains of the endoplasmic reticulum into autophagosomes upon nutrient stress, which then fuse with lysosomes for endoplasmic reticulum turnover. Upon nutrient stress, directly recruits cofactor JMY to the phagophore membrane surfaces and promotes JMY’s actin nucleation activity and autophagosome biogenesis during autophagy.

Subunit / interactions. 3 different light chains, LC1 (a cleavage product of MAP1B), LC2 (a cleavage product of MAP1A) and LC3 (produced by one of the MAP1LC3 genes), can associate with the MAP1A or MAP1B heavy chains. Interacts at microtubules with CABP1 (via EF-hands 1 and 2) but not with calmodulin. Interacts with FYCO1 (via C-terminus). Interacts with TP53INP1 and TP53INP2. Interacts with TBC1D25. Directly interacts with SQSTM1; this interaction leads to MAP1LC3B recruitment to inclusion bodies containing polyubiquitinated protein aggregates and to inclusion body degradation by autophagy. Interacts with ATG4B, MAPK15 and BNIP3. Interacts with MAPB1, KEAP1, PCM1, OFD1, CEP131, and TECPR2. Interacts with TBC1D5. Found in a complex with UBQLN1 and UBQLN2. Interacts with UBQLN4 (via STI1 1 and 2 domains). Interacts with UBQLN1 in the presence of UBQLN4. Interacts with ATG13. Interacts with reticulophagy regulators RETREG1, RETREG2 and RETREG3. No interaction, or very weak, with WDFY3. Interacts with PLCL1; the interaction inhibits autophagosome formation. Interacts with TRIM16. Interacts with CRY1 and PER2. Interacts with the reticulophagy receptor TEX264. Membrane-bound form LC3-II interacts with PHB and PHB2; the interaction takes place upon Parkin-mediated mitochondrial damage. Interacts with PJVK; the interaction is direct. Interacts with KBTBD6 and KBTBD7; the interaction is direct. Interacts with AMBRA1 (via LIR motif). Interacts with JMY; the interaction results in the activation of JYM’s nucleation activity in the cytoplasm. Interacts with MOAP1 (via LIR motif). Interacts with TAX1BP1. Interacts with IRGM. Interacts with STX17. Interacts (the lipidate and non-lipidated LC3 form) with DNM2; this interaction mediates recycling endosome scission leading to autophagosome release. Interacts with IRGQ. (Microbial infection) Interacts with Hantaan hantavirus glycoprotein N; this interaction contributes to the virus-induced degradation of mitochondria by autophagy, which leads to degradation of host MAVS and inhibition of type I interferon (IFN) responses. (Microbial infection) Interacts with Hantaan hantavirus nucleoprotein; this interaction prevents the breakdown of the viral glycoprotein N by virus-triggered autophagy.

Subcellular location. Cytoplasmic vesicle. Autophagosome membrane. Endomembrane system. Mitochondrion membrane. Cytoplasm. Cytoskeleton.

Tissue specificity. Most abundant in heart, brain, skeletal muscle and testis. Little expression observed in liver.

Post-translational modifications. The precursor molecule is cleaved by ATG4 (ATG4A, ATG4B, ATG4C or ATG4D) to expose the glycine at the C-terminus and form the cytosolic form, LC3-I. The processed form is then activated by APG7L/ATG7, transferred to ATG3 and conjugated to phosphatidylethanolamine (PE) phospholipid to form the membrane-bound form, LC3-II. During non-canonical autophagy, the processed form is conjugated to phosphatidylserine (PS) phospholipid. ATG4 proteins also mediate the delipidation of PE-conjugated forms. In addition, ATG4B and ATG4D mediate delipidation of ATG8 proteins conjugated to PS during non-canonical autophagy. ATG4B constitutes the major protein for proteolytic activation. ATG4D is the main enzyme for delipidation activity. (Microbial infection) The Legionella effector RavZ is a deconjugating enzyme that hydrolyzes the amide bond between the C-terminal glycine residue and an adjacent aromatic residue in ATG8 proteins conjugated to phosphatidylethanolamine (PE), producing an ATG8 protein that is resistant to reconjugation by the host machinery due to the cleavage of the reactive C-terminal glycine. RavZ is also able to mediate delipidation of ATG8 proteins conjugated to phosphatidylserine (PS). Phosphorylation by PKA inhibits conjugation of phosphatidylethanolamine (PE). Interaction with MAPK15 reduces the inhibitory phosphorylation and increases autophagy activity. Ubiquitinated by BIRC6; this activity is inhibited by DIABLO/SMAC.

Similarity. Belongs to the ATG8 family.

RefSeq proteins (1): NP_073729* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004241	Atg8-like	Family
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily

Pfam: PF02991

UniProt features (36 total): mutagenesis site 14, strand 8, helix 6, turn 2, lipid moiety-binding region 2, chain 1, propeptide 1, sequence conflict 1, site 1

Structure

Experimental structures (PDB)

50 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
8Q53	X-RAY DIFFRACTION	1.36
6LAN	X-RAY DIFFRACTION	1.41
5D94	X-RAY DIFFRACTION	1.53
5MS5	X-RAY DIFFRACTION	1.53
2ZJD	X-RAY DIFFRACTION	1.56
7GAG	X-RAY DIFFRACTION	1.59
7GAU	X-RAY DIFFRACTION	1.59
7ELG	X-RAY DIFFRACTION	1.6
3VTU	X-RAY DIFFRACTION	1.6
8Q7K	X-RAY DIFFRACTION	1.6
7GAP	X-RAY DIFFRACTION	1.68
7GAO	X-RAY DIFFRACTION	1.69
3VTV	X-RAY DIFFRACTION	1.7
5XAC	X-RAY DIFFRACTION	1.7
7GAM	X-RAY DIFFRACTION	1.75
8YV6	X-RAY DIFFRACTION	1.75
7GAK	X-RAY DIFFRACTION	1.77
7GAF	X-RAY DIFFRACTION	1.84
7GAD	X-RAY DIFFRACTION	1.86
7GA8	X-RAY DIFFRACTION	1.87
5XAD	X-RAY DIFFRACTION	1.88
7GAJ	X-RAY DIFFRACTION	1.89
6J04	X-RAY DIFFRACTION	1.9
5MS6	X-RAY DIFFRACTION	1.9
7GAH	X-RAY DIFFRACTION	1.9
7GAC	X-RAY DIFFRACTION	1.91
7GAL	X-RAY DIFFRACTION	1.91
7GAS	X-RAY DIFFRACTION	1.91
7GAE	X-RAY DIFFRACTION	1.92
7GAI	X-RAY DIFFRACTION	1.97

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZQ8-F1	91.88	0.80

Functional residue map

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

Catalytic / active sites (1): 120–121 (cleavage; by atg4b)

Post-translational modifications (2): 120, 120

Mutagenesis-validated functional residues (14):

Position	Phenotype
52	decreases c18 ceramide binding.
57	increased interaction with wdfy3/alfy, no effect on sqstm1-binding; when associated with k-26 and y-27.
68	impairs cleavage by atg4b.
70	abolishes interaction with tecpr2.
80–82	impaired localization to autophagosomes.
116	abolished delipidation by atg4 family proteins.
119	impaired localization to autophagosomes.
120	no processing of precursor. no lipidation. decreases c18 ceramide binding.
122	no effect on processing of precursor.
26	increased interaction with wdfy3/alfy, no effect on sqstm1-binding; when associated with y-27 and d-57.
27	decreased interaction with legionella effector ravz.
27	increased interaction with wdfy3/alfy, no effect on sqstm1-binding; when associated with k-26 and d-57.
35	decreases c18 ceramide binding.
52–53	no effect on interaction with tecpr2.

Function

Pathways and Gene Ontology

Reactome pathways

27 pathways

ID	Pathway
R-HSA-1632852	Macroautophagy
R-HSA-5205685	PINK1-PRKN Mediated Mitophagy
R-HSA-8854214	TBC/RABGAPs
R-HSA-8934903	Receptor Mediated Mitophagy
R-HSA-9664873	Pexophagy
R-HSA-9679504	Translation of Replicase and Assembly of the Replication Transcription Complex
R-HSA-9694676	Translation of Replicase and Assembly of the Replication Transcription Complex
R-HSA-9754560	SARS-CoV-2 modulates autophagy
R-HSA-9755511	KEAP1-NFE2L2 pathway
R-HSA-9918487	Dengue Virus Genome Translation and Replication
R-HSA-1643685	Disease
R-HSA-199991	Membrane Trafficking
R-HSA-2262752	Cellular responses to stress
R-HSA-5205647	Mitophagy
R-HSA-5653656	Vesicle-mediated transport
R-HSA-5663205	Infectious disease
R-HSA-8953897	Cellular responses to stimuli
R-HSA-9007101	Rab regulation of trafficking
R-HSA-9612973	Autophagy
R-HSA-9663891	Selective autophagy
R-HSA-9678108	SARS-CoV-1 Infection
R-HSA-9679506	SARS-CoV Infections
R-HSA-9694516	SARS-CoV-2 Infection
R-HSA-9705683	SARS-CoV-2-host interactions
R-HSA-9711123	Cellular response to chemical stress
R-HSA-9772572	Early SARS-CoV-2 Infection Events
R-HSA-9824446	Viral Infection Pathways

MSigDB gene sets: 331 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, GOBP_VACUOLE_ORGANIZATION, GOCC_VACUOLAR_MEMBRANE, PEREZ_TP63_TARGETS, ENK_UV_RESPONSE_KERATINOCYTE_UP, REACTOME_MEMBRANE_TRAFFICKING, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, GOBP_MACROAUTOPHAGY, BILD_HRAS_ONCOGENIC_SIGNATURE, MISSIAGLIA_REGULATED_BY_METHYLATION_UP, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN

GO Biological Process (8): autophagosome assembly (GO:0000045), mitophagy (GO:0000423), autophagy (GO:0006914), cellular response to nitrogen starvation (GO:0006995), cellular response to starvation (GO:0009267), macroautophagy (GO:0016236), autophagosome maturation (GO:0097352), autophagy of mitochondrion (GO:0000422)

GO Molecular Function (6): microtubule binding (GO:0008017), phosphatidylethanolamine binding (GO:0008429), ubiquitin protein ligase binding (GO:0031625), ceramide binding (GO:0097001), protein binding (GO:0005515), phospholipid binding (GO:0005543)

GO Cellular Component (13): autophagosome membrane (GO:0000421), mitochondrion (GO:0005739), autophagosome (GO:0005776), cytosol (GO:0005829), microtubule (GO:0005874), axoneme (GO:0005930), endomembrane system (GO:0012505), organelle membrane (GO:0031090), cytoplasmic vesicle (GO:0031410), mitochondrial membrane (GO:0031966), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Mitophagy	2
Selective autophagy	2
Autophagy	1
Rab regulation of trafficking	1
SARS-CoV-1 Infection	1
Early SARS-CoV-2 Infection Events	1
SARS-CoV-2-host interactions	1
Cellular response to chemical stress	1
Dengue Virus Infection	1
Vesicle-mediated transport	1
Cellular responses to stimuli	1
Disease	1
Membrane Trafficking	1
Macroautophagy	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	3
macroautophagy	2
autophagy	2
vacuole	2
Atg12 activating enzyme activity	1
protein-phosphatidylethanolamide deconjugating activity	1
Atg12 conjugating enzyme activity	1
Atg12 ligase activity	1
organelle assembly	1
Atg1/ULK1 kinase complex assembly	1
autophagosome organization	1
autophagy of mitochondrion	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
cellular response to starvation	1
cellular response to nitrogen levels	1
cellular response to nutrient levels	1
cellular response to stress	1
response to starvation	1
autophagosome assembly	1
protein-containing complex disassembly	1
tubulin binding	1
phospholipid binding	1
ubiquitin-like protein ligase binding	1
sphingolipid binding	1
binding	1
lipid binding	1
vacuolar membrane	1
autophagosome	1
intracellular membrane-bounded organelle	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
plasma membrane	1
membrane	1
membrane-bounded organelle	1

Protein interactions and networks

STRING

4328 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAP1LC3B	SQSTM1	Q13501	999
MAP1LC3B	FUNDC1	Q8IVP5	992
MAP1LC3B	CD300C	Q08708	972
MAP1LC3B	ATG5	Q9H1Y0	962
MAP1LC3B	ATG3	Q9NT62	956
MAP1LC3B	ATG7	O95352	954
MAP1LC3B	ATG4B	Q9Y4P1	949
MAP1LC3B	BECN1	Q14457	943
MAP1LC3B	MAP1S	Q66K74	933
MAP1LC3B	FYCO1	Q9BQS8	930
MAP1LC3B	MAP1A	P78559	919
MAP1LC3B	CAV1	Q03135	917
MAP1LC3B	BNIP3	Q12983	916
MAP1LC3B	ULK1	O75385	914
MAP1LC3B	ATG12	O94817	913

IntAct

343 interactions, top by confidence:

A	B	Type	Score
MAP1LC3B	SQSTM1	psi-mi:“MI:0407”(direct interaction)	0.980
SQSTM1	MAP1LC3B	psi-mi:“MI:0915”(physical association)	0.980
MAP1LC3B	SQSTM1	psi-mi:“MI:0914”(association)	0.980
MAP1LC3B	SQSTM1	psi-mi:“MI:0915”(physical association)	0.980
SQSTM1	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.980
MAP1LC3B	ATG4B	psi-mi:“MI:0915”(physical association)	0.950
ATG4B	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.950
KBTBD7	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.840
MAP1LC3B	KBTBD7	psi-mi:“MI:0915”(physical association)	0.840
MAP1LC3B	ATG3	psi-mi:“MI:0407”(direct interaction)	0.800
MAP1LC3B	FUNDC1	psi-mi:“MI:0915”(physical association)	0.780
FUNDC1	MAP1LC3B	psi-mi:“MI:0915”(physical association)	0.780
MAP1LC3B	FUNDC1	psi-mi:“MI:0403”(colocalization)	0.780
MAP1LC3B	NBR1	psi-mi:“MI:0915”(physical association)	0.770
NBR1	MAP1LC3B	psi-mi:“MI:0915”(physical association)	0.770
MAP1LC3B	NBR1	psi-mi:“MI:0407”(direct interaction)	0.770
NBR1	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.770

BioGRID (784): TP53 (Affinity Capture-Western), MAP1LC3B (Two-hybrid), MAP1LC3B (Two-hybrid), MAP1LC3B (Two-hybrid), FUNDC1 (Two-hybrid), MAP1LC3B (Reconstituted Complex), MAP1LC3B (Reconstituted Complex), TBK1 (Reconstituted Complex), MAP1LC3B (Synthetic Rescue), MAP1LC3B (Two-hybrid), MAP1LC3B (Affinity Capture-Western), MAP1LC3B (Affinity Capture-Western), MAP1LC3B (Affinity Capture-Western), KBTBD7 (Reconstituted Complex), KBTBD6 (Reconstituted Complex)

ESM2 similar proteins: A1CQS1, A1D3N4, A2XXR7, A2YAG8, A2YS06, A6NCE7, A6RPU4, A7KAL9, I1S1W5, J4UTT5, M1C146, M2SQA5, N4X184, O41515, P0CM28, P0CM29, P60519, P60520, P60521, P60522, Q0C804, Q0V3Y9, Q1E4K5, Q1SF86, Q2HJ23, Q2RBS4, Q2UBH5, Q2XPP5, Q4P2U6, Q4WJ27, Q69NP0, Q69RC4, Q6XVN8, Q6Z1D5, Q7XPR1, Q86CR8, Q8J282, Q8LEM4, Q8S924, Q8S925

Diamond homologs: A0A1B7XV12, A1CQS1, A1D3N4, A2QPN1, A2XXR7, A2YS06, A3GFU8, A4LA70, A5DWI6, A6NCE7, A6RPU4, A6ZKM4, A7E8H4, A7KAL9, A7TDU7, C4B4E4, I1S1W5, J4UTT5, M1C146, M2SQA5, N4X184, O41515, O94272, O95166, P0C075, P0CO54, P0CO55, P38182, P60517, P60518, P60519, P60520, P60521, P60522, P87068, Q09490, Q0C804, Q0V3Y9, Q0VGK0, Q1E4K5

SIGNOR signaling

17 interactions.

A	Effect	B	Mechanism
ATG4B	up-regulates	MAP1LC3B	cleavage
MAP1LC3B	up-regulates	SQSTM1	binding
MAP1LC3B	down-regulates	NBR1	binding
MAP1LC3B	up-regulates	ATG3	binding
ATG7	up-regulates	MAP1LC3B	binding
TP53INP1	up-regulates	MAP1LC3B	binding
MAP1LC3B	up-regulates	Autophagosome_formation
FYCO1	“up-regulates activity”	MAP1LC3B	binding
TRAF6	“down-regulates quantity by destabilization”	MAP1LC3B	polyubiquitination
GDNF	“up-regulates quantity by expression”	MAP1LC3B	“transcriptional regulation”
ADNP	“up-regulates activity”	MAP1LC3B	binding
NEK9	“down-regulates activity”	MAP1LC3B	phosphorylation
STK3/4	“down-regulates activity”	MAP1LC3B	phosphorylation
PRKCZ	“down-regulates activity”	MAP1LC3B	phosphorylation
TFEB	“up-regulates quantity by expression”	MAP1LC3B	“transcriptional regulation”
ACSS2	“up-regulates quantity by expression”	MAP1LC3B	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 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
Macroautophagy	12	24.7×	2e-11
Autophagy	9	23.8×	2e-08

GO biological processes:

GO term	Partners	Fold	FDR
piecemeal microautophagy of the nucleus	7	86.2×	3e-10
reticulophagy	7	64.7×	2e-09
mitophagy	14	58.6×	8e-19
autophagy of mitochondrion	5	48.2×	6e-06
autophagosome assembly	13	38.4×	5e-15
macroautophagy	9	28.5×	5e-09
positive regulation of autophagy	8	21.9×	5e-07
autophagy	9	13.0×	4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

761 predictions. Top by Δscore:

Variant	Effect	Δscore
16:87392466:CGG:C	donor_loss	1.0000
16:87392467:GGTG:G	donor_loss	1.0000
16:87392468:GTGA:G	donor_loss	1.0000
16:87398813:A:AG	acceptor_gain	1.0000
16:87398814:G:GA	acceptor_gain	1.0000
16:87398868:CCGG:C	donor_loss	1.0000
16:87398871:G:GA	donor_loss	1.0000
16:87398871:G:GG	donor_gain	1.0000
16:87398872:T:G	donor_loss	1.0000
16:87402170:TCCA:T	acceptor_loss	1.0000
16:87402171:CCA:C	acceptor_loss	1.0000
16:87402172:CAG:C	acceptor_loss	1.0000
16:87402173:A:AG	acceptor_gain	1.0000
16:87402173:AGGT:A	acceptor_gain	1.0000
16:87402174:G:GG	acceptor_gain	1.0000
16:87402174:GGT:G	acceptor_gain	1.0000
16:87402174:GGTG:G	acceptor_gain	1.0000
16:87402174:GGTGA:G	acceptor_gain	1.0000
16:87402258:GA:G	donor_gain	1.0000
16:87402260:G:GG	donor_gain	1.0000
16:87402274:A:G	donor_gain	1.0000
16:87402277:ATTAG:A	donor_loss	1.0000
16:87402278:T:G	donor_gain	1.0000
16:87402278:T:TG	donor_gain	1.0000
16:87402278:TTAG:T	donor_loss	1.0000
16:87402279:TAG:T	donor_loss	1.0000
16:87402280:AG:A	donor_loss	1.0000
16:87402281:GG:G	donor_loss	1.0000
16:87402283:T:A	donor_loss	1.0000
16:87402918:A:AG	acceptor_gain	1.0000

AlphaMissense

823 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:87398822:A:C	R16S	1.000
16:87398822:A:T	R16S	1.000
16:87402179:T:A	I34K	1.000
16:87402231:G:C	K51N	1.000
16:87402231:G:T	K51N	1.000
16:87402232:T:C	F52L	1.000
16:87402233:T:C	F52S	1.000
16:87402234:C:A	F52L	1.000
16:87402234:C:G	F52L	1.000
16:87402236:T:C	L53P	1.000
16:87402266:T:C	L63P	1.000
16:87403041:T:C	F108L	1.000
16:87403043:C:A	F108L	1.000
16:87403043:C:G	F108L	1.000
16:87392446:T:C	F7L	0.999
16:87392448:C:A	F7L	0.999
16:87392448:C:G	F7L	0.999
16:87398821:G:C	R16T	0.999
16:87398821:G:T	R16I	0.999
16:87398864:A:C	K30N	0.999
16:87398864:A:T	K30N	0.999
16:87398869:C:A	P32Q	0.999
16:87402176:T:A	V33E	0.999
16:87402179:T:G	I34R	0.999
16:87402182:T:A	I35K	0.999
16:87402209:T:A	L44H	0.999
16:87402209:T:C	L44P	0.999
16:87402224:A:T	K49I	0.999
16:87402225:A:C	K49N	0.999
16:87402225:A:T	K49N	0.999

dbSNP variants (sampled 300 via entrez): RS1000188528 (16:87399698 G>C), RS1000297222 (16:87394932 T>TA), RS1000355520 (16:87391323 A>C,G), RS1000551172 (16:87394502 C>G), RS1000974116 (16:87390787 G>A), RS1001052591 (16:87398182 C>G), RS1001219263 (16:87399973 C>T), RS1001328299 (16:87395195 C>G,T), RS1001507647 (16:87398828 A>T), RS1001544173 (16:87403843 C>T), RS1001576215 (16:87399837 G>A,C,T), RS1001600965 (16:87398993 C>A,T), RS1001785616 (16:87395437 A>G), RS1001809033 (16:87394561 C>T), RS1001847653 (16:87403682 C>G,T)

Disease associations

OMIM: gene MIM:609604 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001469_5	Major depressive disorder	5.000000e-06
GCST005232_16	Neuroticism	1.000000e-06
GCST007709_135	General factor of neuroticism	8.000000e-09
GCST009391_194	Metabolite levels	9.000000e-06
GCST010002_117	Refractive error	6.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007660	neuroticism measurement
EFO:0010482	gamma-aminoisobutyric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (20): CHEMBL4879514 (SINGLE PROTEIN), CHEMBL5482984 (PROTEIN-PROTEIN INTERACTION), CHEMBL6066839 (PROTEIN-PROTEIN INTERACTION), CHEMBL6066860 (PROTEIN-PROTEIN INTERACTION), CHEMBL6193844 (PROTEIN-PROTEIN INTERACTION), CHEMBL6193845 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195576 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195577 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195578 (PROTEIN-PROTEIN INTERACTION), CHEMBL6195579 (PROTEIN-PROTEIN INTERACTION)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 11,401 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL36506	NOVOBIOCIN	4	11,401

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
N-(1-adamantyl)-2-[4-[2-[(2-hydroxy-4,4-dimethyl-6-oxocyclohexen-1-yl)methylideneamino]ethyl]piperazin-1-yl]acetamide	IC50	550000 nM	US-11529321: Use of aminomethylenecyclohexane-1,3-dione compound

ChEMBL bioactivities

198 potent at pChembl≥5 of 267 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.12	IC50	7.6	nM	CHEMBL5556385
7.76	IC50	17.4	nM	CHEMBL5556385
7.47	IC50	33.6	nM	CHEMBL5560804
7.29	IC50	51.7	nM	CHEMBL5563109
7.25	IC50	56.46	nM	CHEMBL5556385
7.10	IC50	80	nM	CHEMBL5556385
7.00	Kd	100	nM	CHEMBL72365
7.00	Kd	100	nM	CHEMBL5288592
7.00	IC50	100	nM	CHEMBL5560804
6.85	IC50	140	nM	CHEMBL5563109
6.76	Kd	175	nM	CHEMBL5180355
6.73	Kd	187	nM	CHEMBL5439010
6.70	IC50	200	nM	CHEMBL5285058
6.70	IC50	200	nM	CHEMBL600635
6.70	IC50	200	nM	CHEMBL5561502
6.70	IC50	200	nM	CHEMBL5563109
6.66	IC50	220	nM	CHEMBL5565069
6.56	IC50	275	nM	CHEMBL5780106
6.56	IC50	275	nM	CHEMBL5862727
6.56	IC50	275	nM	CHEMBL5761708
6.56	IC50	275	nM	CHEMBL5916198
6.56	IC50	275	nM	CHEMBL6039270
6.56	IC50	275	nM	CHEMBL5804170
6.56	IC50	275	nM	CHEMBL5994319
6.56	IC50	275	nM	CHEMBL5780498
6.56	IC50	275	nM	CHEMBL5815465
6.56	IC50	275	nM	CHEMBL5764459
6.56	IC50	275	nM	CHEMBL6037868
6.56	IC50	275	nM	CHEMBL5988880
6.56	IC50	275	nM	CHEMBL6057680
6.56	IC50	275	nM	CHEMBL6065218
6.56	IC50	275	nM	CHEMBL5941263
6.56	IC50	275	nM	CHEMBL6003912
6.56	IC50	275	nM	CHEMBL5989894
6.56	IC50	275	nM	CHEMBL5863478
6.56	IC50	275	nM	CHEMBL5922669
6.56	IC50	275	nM	CHEMBL5909955
6.56	IC50	275	nM	CHEMBL5853062
6.56	IC50	275	nM	CHEMBL6062477
6.56	IC50	275	nM	CHEMBL5884677
6.56	IC50	275	nM	CHEMBL5969859
6.56	IC50	275	nM	CHEMBL5909720
6.56	IC50	275	nM	CHEMBL5829143
6.56	IC50	275	nM	CHEMBL5866926
6.56	IC50	275	nM	CHEMBL5921411
6.56	IC50	275	nM	CHEMBL5812007
6.56	IC50	275	nM	CHEMBL6048672
6.56	IC50	275	nM	CHEMBL6006975
6.56	IC50	275	nM	CHEMBL5876621
6.56	IC50	275	nM	CHEMBL5970022

PubChem BioAssay actives

57 with measured affinity, of 296 total; 48 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
5-(5,6-dichloro-1H-indol-4-yl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086240: Inhibition of GST-tagged LC3B (unknown origin) using biotin-labeled LBP2 as substrate preincubated with compound for 12 hrs followed by substrate addition and measured after 2 hrs by Alphascreen assay	ic50	0.0076	uM
5-(2,3-dichlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086240: Inhibition of GST-tagged LC3B (unknown origin) using biotin-labeled LBP2 as substrate preincubated with compound for 12 hrs followed by substrate addition and measured after 2 hrs by Alphascreen assay	ic50	0.0336	uM
5-(2,3-dichlorophenyl)-3-hydroxy-2-(2-morpholin-4-ylethyliminomethyl)cyclohex-2-en-1-one	2086240: Inhibition of GST-tagged LC3B (unknown origin) using biotin-labeled LBP2 as substrate preincubated with compound for 12 hrs followed by substrate addition and measured after 2 hrs by Alphascreen assay	ic50	0.0517	uM
N-(3-aminopropyl)-N-[(1R)-1-(3-benzyl-7-iodo-4H-quinazolin-2-yl)-2-methylpropyl]-4-methylbenzamide	1922362: Binding affinity to LC3B (unknown origin) assessed as dissociation constant	kd	0.1000	uM
(3Z)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-1H-indol-2-one	1922362: Binding affinity to LC3B (unknown origin) assessed as dissociation constant	kd	0.1000	uM
N-[(1R)-1-(3-benzyl-7-chloro-4-oxoquinazolin-2-yl)-2-methylpropyl]-N-[3-[(3’,6’-dihydroxy-3-oxospiro[2-benzofuran-1,9’-xanthene]-5-yl)carbamothioylamino]propyl]-4-methylbenzamide	1910890: Binding affinity to human recombinant LC3B assessed as dissociation constant incubated for 30 mins by fluorescence anisotropy assay	kd	0.1750	uM
N-[6-[[2-[2,6-dibromo-4-[(Z)-(5-iodo-2-oxo-1H-indol-3-ylidene)methyl]phenoxy]acetyl]amino]hexyl]-4-[3,4-dimethyl-2-(4-methylphenyl)-7-oxopyrazolo[3,4-d]pyridazin-6-yl]butanamide	2005777: Binding affinity to LC3-B (unknown origin) assessed as dissociation constant by MST analysis	kd	0.1870	uM
5-(2,6-dichlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.2000	uM
(3Z)-5-bromo-3-[(3-bromo-4,5-dihydroxyphenyl)methylidene]-1H-indol-2-one	2067064: Inhibition of human LC3B expressed in Escherichia coli BL21 (DE3)	ic50	0.2000	uM
5,7-dihydroxy-4-phenylchromen-2-one	2067064: Inhibition of human LC3B expressed in Escherichia coli BL21 (DE3)	ic50	0.2000	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(2,3,5-trichlorophenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.2200	uM
5-(2-chlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.2900	uM
5-(2-bromophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.3000	uM
5-(2,4-dichlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.3100	uM
5-(3-chlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.3700	uM
5-(2,5-dichlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.4000	uM
2-[2-(dimethylamino)ethyliminomethyl]-5-(2-fluorophenyl)-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.4400	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(1H-indol-4-yl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.4400	uM
5-(3-bromophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.4900	uM
2-[2-(dimethylamino)ethyliminomethyl]-5-(3-fluorophenyl)-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.6100	uM
N-[2-[2-[2-[2-[4-(3-chloro-4-fluoroanilino)-7-methoxyquinazolin-6-yl]oxyethoxy]ethoxy]ethoxy]ethyl]-2-[2,6-dibromo-4-[(Z)-(5-iodo-2-oxo-1H-indol-3-ylidene)methyl]phenoxy]acetamide	2062549: Binding affinity to biotinylated LC3B/EGFR in human HCC827 cells assessed as dissociation constant BLI assay	kd	0.7100	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(3-methylphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.8700	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(2-methylphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.9200	uM
5-(4-chlorophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.9400	uM
5-(4-bromophenyl)-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	0.9500	uM
N-[(1R)-1-(3-benzyl-7-chloro-4-oxoquinazolin-2-yl)-2-methylpropyl]-4-methyl-N-[3-[9-[4-[4-(pyridin-3-ylmethylcarbamothioylamino)phenyl]sulfonylpiperazin-1-yl]nonanoylamino]propyl]benzamide	1910893: Binding affinity to LC3B (unknown origin) assessed as dissociation constant by surface plasmon resonance analysis	kd	0.9930	uM
3-hydroxy-5-(4-methylphenyl)-2-(2-piperidin-1-ylethyliminomethyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.2100	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(4-methylphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.2100	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-phenylcyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.2600	uM
2-[2-(dimethylamino)ethyliminomethyl]-5-(4-fluorophenyl)-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.2600	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(3-methoxyphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.2700	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(2-methoxyphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.6600	uM
3-hydroxy-5-(4-methylphenyl)-2-(2-morpholin-4-ylethyliminomethyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.8100	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-(4-methoxyphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	1.8500	uM
N-[2-[2-[4-(3-chloro-4-fluoroanilino)-7-methoxyquinazolin-6-yl]oxyethoxy]ethyl]-2-[2,6-dibromo-4-[(Z)-(2-oxo-1H-indol-3-ylidene)methyl]phenoxy]acetamide	2062549: Binding affinity to biotinylated LC3B/EGFR in human HCC827 cells assessed as dissociation constant BLI assay	kd	2.2000	uM
2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxy-5-thiophen-2-ylcyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	2.3200	uM
1-[4-[2-[2-[2-[2-[(3E)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-2-oxoindol-1-yl]ethoxy]ethoxy]ethoxy]ethoxy]phenyl]sulfonyl-3-(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)urea	2116258: Binding affinity to CM5 chip-immobilized LC3B (unknown origin) assessed as dissociation constant by SPR analysis	kd	3.5480	uM
N-[4-hydroxy-7-(naphthalen-1-ylsulfonylamino)-2-oxochromen-3-yl]-3-(3-methylbutyl)benzamide	1775857: Displacement of sGFP-p62-LIR peptide from human N-terminal SNAP-fused LC3B by time-resolved FRET assay	ki	4.2000	uM
2-[7-[4-[(3Z)-5-bromo-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-2-oxoindol-1-yl]butoxy]-6-methoxy-1-methyl-3,4-dihydro-2H-isoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide	2097353: Binding affinity to His-tagged LC3B (unknown origin) coupled to CM5 chip assessed as dissociation constant by SPR analysis	kd	5.6900	uM
3-hydroxy-5-(4-methylphenyl)-2-(2-piperazin-1-ylethyliminomethyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	6.8000	uM
N-[4-hydroxy-2-oxo-7-(2-phenylethylsulfonylamino)chromen-3-yl]-3-(3-methylbutyl)benzamide	1775857: Displacement of sGFP-p62-LIR peptide from human N-terminal SNAP-fused LC3B by time-resolved FRET assay	ki	7.4000	uM
2-[3-(dimethylamino)propyliminomethyl]-3-hydroxy-5-(4-methylphenyl)cyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	7.7700	uM
[(3R,4S,5R,6R)-5-hydroxy-6-[4-hydroxy-3-[[4-hydroxy-3-(3-methylbutyl)benzoyl]amino]-8-methyl-2-oxochromen-7-yl]oxy-3-methoxy-2,2-dimethyloxan-4-yl] carbamate	1775857: Displacement of sGFP-p62-LIR peptide from human N-terminal SNAP-fused LC3B by time-resolved FRET assay	ki	8.1000	uM
5-cyclohexyl-2-[2-(dimethylamino)ethyliminomethyl]-3-hydroxycyclohex-2-en-1-one	2086239: Inhibition of N-terminal GST-tagged LC3B (unknown origin) measured for 18 hrs by fluorescence polarization assay	ic50	8.1400	uM
2-[7-[4-[(3Z)-5-bromo-3-[(3-bromo-4-hydroxy-5-methoxyphenyl)methylidene]-2-oxoindol-1-yl]butoxy]-6-methoxy-1-methyl-3,4-dihydro-2H-isoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide	2097353: Binding affinity to His-tagged LC3B (unknown origin) coupled to CM5 chip assessed as dissociation constant by SPR analysis	kd	8.4770	uM
2-[7-[2-[2-[(3Z)-5-bromo-3-[(3-bromo-4-hydroxy-5-methoxyphenyl)methylidene]-2-oxoindol-1-yl]ethoxy]ethoxy]-6-methoxy-1-methyl-3,4-dihydro-2H-isoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide	2097353: Binding affinity to His-tagged LC3B (unknown origin) coupled to CM5 chip assessed as dissociation constant by SPR analysis	kd	9.7980	uM
2-[7-[2-[2-[(3Z)-5-bromo-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-2-oxoindol-1-yl]ethoxy]ethoxy]-6-methoxy-1-methyl-3,4-dihydro-2H-isoquinolin-1-yl]-N-(1,3-thiazol-2-yl)acetamide	2097353: Binding affinity to His-tagged LC3B (unknown origin) coupled to CM5 chip assessed as dissociation constant by SPR analysis	kd	9.8770	uM
N-[4-hydroxy-7-[(4-methylphenyl)sulfonylamino]-2-oxochromen-3-yl]-3-(3-methylbutyl)benzamide	1775857: Displacement of sGFP-p62-LIR peptide from human N-terminal SNAP-fused LC3B by time-resolved FRET assay	ki	10.0000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Chloroquine	increases lipidation, decreases reaction, affects lipidation, increases reaction, affects localization (+6 more)	39
3-methyladenine	affects lipidation, affects cotreatment, increases cleavage, increases localization, increases reaction (+7 more)	32
bafilomycin A1	increases expression, increases reaction, affects reaction, increases metabolic processing, affects cotreatment (+4 more)	19
Acetylcysteine	increases reaction, increases expression, increases metabolic processing, increases cleavage, decreases reaction (+3 more)	18
sodium arsenite	affects reaction, affects binding, decreases expression, increases abundance, decreases reaction (+3 more)	17
Sirolimus	increases cleavage, increases reaction, affects cotreatment, increases expression, affects reaction (+3 more)	17
Arsenic Trioxide	increases cleavage, increases lipidation, affects localization, increases metabolic processing, decreases reaction (+3 more)	8
bisphenol A	decreases reaction, affects cotreatment, increases expression, increases reaction, increases lipidation (+4 more)	6
4-phenylbutyric acid	decreases expression, decreases reaction, increases expression, increases lipidation	6
dorsomorphin	decreases lipidation, decreases reaction, affects reaction, increases lipidation, affects metabolic processing	6
Cisplatin	increases expression, increases reaction, increases phosphorylation, affects cotreatment, increases lipidation (+1 more)	6
Cadmium Chloride	decreases reaction, increases abundance, increases phosphorylation, increases expression, increases metabolic processing (+2 more)	6
Particulate Matter	increases abundance, decreases expression, increases reaction, affects cotreatment, decreases reaction (+2 more)	6
Doxorubicin	decreases reaction, increases lipidation, affects cotreatment, increases expression, increases reaction	5
Hydrogen Peroxide	affects reaction, increases abundance, increases lipidation, increases reaction, decreases reaction (+4 more)	5
Tobacco Smoke Pollution	increases reaction, decreases expression, affects binding, decreases reaction, increases expression (+1 more)	5
Valproic Acid	affects expression, increases expression	5
Cyclosporine	affects cotreatment, increases expression	5
trichostatin A	affects expression, affects localization, increases cleavage, increases expression	4
bafilomycin A	increases expression, increases reaction, increases lipidation, increases cleavage, affects reaction (+1 more)	4
U 0126	decreases expression, decreases reaction, increases expression, increases lipidation	4
Resveratrol	affects cotreatment, decreases reaction, increases expression, affects metabolic processing, affects reaction (+2 more)	4
Vorinostat	increases reaction, affects localization, decreases reaction, increases expression, increases cleavage	4
Ammonium Chloride	increases lipidation, increases metabolic processing, affects reaction, increases expression	4
Arsenic	increases reaction, increases abundance, increases lipidation, increases expression	4
Tunicamycin	decreases reaction, increases expression, increases prenylation	4
methylmercuric chloride	increases expression	3
pepstatin	increases reaction, decreases degradation, affects cotreatment, decreases reaction, increases degradation (+2 more)	3
benzyloxycarbonylleucyl-leucyl-leucine aldehyde	decreases reaction, increases expression, increases lipidation, affects reaction, increases phosphorylation	3
aloxistatin	decreases reaction, increases degradation, increases lipidation, increases expression, increases reaction (+2 more)	3

ChEMBL screening assays

153 unique, capped per target: 153 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4835339	Binding	Binding affinity to recombinant LC3B (unknown origin) assessed as shift of melting temperature by differential scanning fluorimetry	Demonstrating Ligandability of the LC3A and LC3B Adapter Interface. — J Med Chem

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_0A24	TZM-tfLC3B	Cancer cell line	Female
CVCL_A8BZ	THP1-Difluo hLC3	Cancer cell line	Male
CVCL_A8CA	HeLa-Difluo hLC3	Cancer cell line	Female
CVCL_E8GV	HEK293 ATG2A/ATG2B DKO GFP-ATG2A TagBFP-LC3B	Transformed cell line	Female
CVCL_SW32	HAP1 MAP1LC3B (-) 1	Cancer cell line	Male
CVCL_SW33	HAP1 MAP1LC3B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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