ATG4B

Summary

ATG4B (autophagy related 4B cysteine peptidase, HGNC:20790) is a protein-coding gene on chromosome 2q37.3, encoding Cysteine protease ATG4B (Q9Y4P1). Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins.

Autophagy is the process by which endogenous proteins and damaged organelles are destroyed intracellularly. Autophagy is postulated to be essential for cell homeostasis and cell remodeling during differentiation, metamorphosis, non-apoptotic cell death, and aging. Reduced levels of autophagy have been described in some malignant tumors, and a role for autophagy in controlling the unregulated cell growth linked to cancer has been proposed. This gene encodes a member of the autophagin protein family. The encoded protein is also designated as a member of the C-54 family of cysteine proteases. Alternate transcriptional splice variants, encoding different isoforms, have been characterized.

Source: NCBI Gene 23192 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 108 total — 3 pathogenic, 1 likely-pathogenic
• Druggable target: yes — 7 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_013325

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20790
Approved symbol	ATG4B
Name	autophagy related 4B cysteine peptidase
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	Apg4B, KIAA0943, DKFZp586D1822, AUTL1
Ensembl gene	ENSG00000168397
Ensembl biotype	protein_coding
OMIM	611338
Entrez	23192

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 20 protein_coding, 15 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000344376, ENST00000400771, ENST00000400772, ENST00000402096, ENST00000404914, ENST00000405546, ENST00000415107, ENST00000419606, ENST00000425239, ENST00000428861, ENST00000429899, ENST00000430617, ENST00000460211, ENST00000465399, ENST00000468018, ENST00000475195, ENST00000475693, ENST00000479554, ENST00000479941, ENST00000482507, ENST00000483778, ENST00000491867, ENST00000493618, ENST00000494132, ENST00000494465, ENST00000902605, ENST00000902606, ENST00000902607, ENST00000902608, ENST00000902609, ENST00000902610, ENST00000902611, ENST00000929774, ENST00000929775, ENST00000929776, ENST00000929777, ENST00000951473, ENST00000951474, ENST00000951475, ENST00000951476

RefSeq mRNA: 2 — MANE Select: NM_013325 NM_013325, NM_178326

CCDS: CCDS46564, CCDS46565

Canonical transcript exons

ENST00000404914 — 13 exons

Exon	Start	End
ENSE00001834087	241672191	241673857
ENSE00003470907	241655271	241655343
ENSE00003495068	241666645	241666838
ENSE00003547072	241668540	241668685
ENSE00003548330	241671312	241671405
ENSE00003568388	241670726	241670782
ENSE00003612787	241653512	241653610
ENSE00003619396	241651264	241651335
ENSE00003655433	241654546	241654647
ENSE00003677093	241651010	241651111
ENSE00003784171	241659108	241659187
ENSE00003789869	241668143	241668221
ENSE00003846382	241637693	241637724

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 98.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5347 / max 191.9413, expressed in 1806 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
26546	18.0189	1803
26545	2.4688	1181
26547	0.0469	16

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	98.49	gold quality
cerebellar hemisphere	UBERON:0002245	98.22	gold quality
cerebellar cortex	UBERON:0002129	98.11	gold quality
metanephros cortex	UBERON:0010533	97.91	gold quality
adenohypophysis	UBERON:0002196	97.66	gold quality
right lobe of thyroid gland	UBERON:0001119	97.64	gold quality
left testis	UBERON:0004533	97.62	gold quality
left lobe of thyroid gland	UBERON:0001120	97.49	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.44	gold quality
body of uterus	UBERON:0009853	97.43	gold quality
endocervix	UBERON:0000458	97.42	gold quality
right ovary	UBERON:0002118	97.38	gold quality
left ovary	UBERON:0002119	97.36	gold quality
mucosa of transverse colon	UBERON:0004991	97.31	gold quality
right testis	UBERON:0004534	97.30	gold quality
gall bladder	UBERON:0002110	97.29	gold quality
mucosa of stomach	UBERON:0001199	97.22	gold quality
stromal cell of endometrium	CL:0002255	97.18	gold quality
lower esophagus mucosa	UBERON:0035834	97.17	gold quality
right uterine tube	UBERON:0001302	97.14	gold quality
tibial nerve	UBERON:0001323	97.12	gold quality
transverse colon	UBERON:0001157	97.11	gold quality
pituitary gland	UBERON:0000007	96.90	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.86	gold quality
lower esophagus	UBERON:0013473	96.85	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.84	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.84	gold quality
cerebellum	UBERON:0002037	96.78	gold quality
body of stomach	UBERON:0001161	96.72	gold quality
ectocervix	UBERON:0012249	96.72	gold quality

Single-cell (SCXA)

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

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

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1, EGR1

miRNA regulators (miRDB)

35 targeting ATG4B, 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-4776-3P	100.00	68.73	1340
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-6760-5P	98.87	66.73	1515
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-6793-3P	97.66	65.78	1084

Literature-anchored findings (GeneRIF, showing 40)

• HsAtg4B negatively regulates the localization of LC3 to a membrane compartment by delipidation (PMID:15187094)
• analysis of specificity and catalysis of HsAtg4B (PMID:16183633)
• crystal structure of human Atg4b by X-ray crystallography at 2.0 A resolution, and show that Atg4b is a cysteine protease whose active catalytic triad site consists of Cys74, His280 and Asp278 (PMID:16325851)
• Murine Atg8L/Apg8L modification is mediated by human Atg4B. (PMID:16704426)
• The crystal structures of catalytically inert human Atg4B in complex with processed and unprocessed forms of LC3 showed that, on LC3 binding, the regulatory loop and the N-terminal tail of HsAtg4B undergo large conformational changes. (PMID:19322194)
• Atg4B possessed the broadest spectrum against all substrates, followed by Atg4A for ATG8 substrates (PMID:21177865)
• The actions of ATG4 family members (particularly ATG4B) are required for the control of autophagosome fusion with late, degradative compartments in differentiating human erythroblasts. (PMID:23508006)
• This study identifies ATG4B as a potential biomarker for predicting therapeutic response in treatment-naive chronic myeloid leukemia stem/progenitor cells and uncovers ATG4B as a possible drug target in these cells. (PMID:24755409)
• ATG4B independently plays a role as a positive regulator on tumor proliferation and a negative regulator on autophagy in colorectal cancer cells. (PMID:24991826)
• Purified ATG4B protein interact with LC3B in vitro. (PMID:25652856)
• Results demonstrated that upregulation of miR-34a by transfection or demethylation resulted in the enhanced apoptosis and drug sensitivity in prostate cancer cells. ATG4B, directly regulated by miR-34a through AMPK/mTOR, was involved in this process. (PMID:26499184)
• The results have interesting implications that SLC27A4/ATG4B complex might be conducive to the occurrence of autophagy in human cancer cells, which is meaningful investigations toward the aim of developing autophagy-targeting drugs and have significant values in clinical application. (PMID:26662804)
• O-GlcNAcylation of ATG4B regulates autophagy activation by increasing its proteolytic activity under metabolic stress condition (PMID:27527864)
• these results demonstrate a novel association of ATG4B positive expression with HER2 positive breast cancers (PMID:27556700)
• MIRlet-7i is able to regulate autophagic activity via regulating Atg4B expression, which might contribute to the pathogenesis of pre-eclampsia. (PMID:27770612)
• The structure and regulatory machinery of Atg4b [review] (PMID:28253956)
• ATG4B contains a C-terminal LIR motif important for binding and efficient cleavage of mammalian orthologs of yeast Atg8 (PMID:28287329)
• Data show that ULK1, a protein kinase activated at the autophagosome formation site, phosphorylates human ATG4B on serine 316. (PMID:28821708)
• study demonstrates that Rab7b regulates LC3 processing by modulating Atg4B activity; taken together, findings reveal Rab7b as a novel negative regulator of autophagy through its interaction with Atg4B (PMID:28835545)
• Reporter assay showed that HSF1 increased the transcriptional activity of ATG4B gene promoter, and chromatin immunoprecipitation assay verified that HSF1 bound to the site (-1429 to -1417) in ATG4B gene promoter region. (PMID:28889000)
• ATG4B expression was observed markedly upregulated by EWS-FLI1 overexpression, and silencing of ATG4B dramatically inhibits autophagy in Ewing sarcoma cells. (PMID:28902354)
• that the phosphorylation of ATG4B at Ser34 participates in the metabolic reprogramming of hepatocellular carcinoma cells via repressing mitochondrial function (PMID:29165041)
• Knockdown of ATG4B had only a minor effect on AMPK activation and G1 phase arrest in liver kinase B1-deficient or AMPK-inhibited cancer cells. (PMID:29169176)
• Our work describes an MST4-ATG4B signaling axis that influences glioblastoma autophagy and malignancy (PMID:29232556)
• miR-665-3p regulates autophagy by targeting ATG4B expression to relieve inflammation and apoptosis in intestinal ischemia/reperfusion. (PMID:29706629)
• hese findings suggest that LV-320 will serve as a relevant chemical tool to study the various roles of ATG4B in cancer and other contexts. (PMID:30076329)
• our results demonstrated that the interaction of Atg4B and Bcl-2 might play an important role in Cd-induced crosstalk between apoptosis and autophagy through disassociation of Bcl-2-Beclin1. Cd-induced autophagy is apoptosis-dependent and prevents apoptotic cell death to ensure the growth and proliferation of A549 cells. (PMID:30458278)
• Human HAP1 and HeLa cells lacking ATG4B exhibit a severe but incomplete defect in LC3/GABARAP processing and autophagy. By further genetic depletion of ATG4 isoforms using CRISPR-Cas9 and siRNA we uncover that ATG4A, ATG4C and ATGD all contribute to residual priming activity, which is sufficient to enable lipidation of endogenous GABARAPL1 on autophagic structures. (PMID:30661429)
• ERBB2 might modulate ATG4B for autophagy induction in oxidative stress-stimulated ARPE-19 cells. ERBB2 knockdown also caused an accumulation of nuclear factor erythroid 2-related factor 2 (NRF2) and enhanced its transcriptional activity. (PMID:30870514)
• Autophagy-related 4 cysteine peptidase (ATG4) proteases process inactive pro-LC3/GABARAP before lipidation, and the same proteases can also deconjugate LC3/GABARAP from lipids. (PMID:31315929)
• the importance of the regulatory axis of SNHG16/miR-16/ATG4B underlying osteosarcoma progression and chemoresistance to cisplatin. (PMID:31427084)
• Virus-encoded proteases play diverse roles in the efficient replication of enterovirus 71 (EV71), which is the causative agent of human hand, foot, and mouth disease (HFMD). ATG4B protein processes the viral polyprotein with its cysteine protease activity and helps EV71 replicate through a chemical biology strategy. (PMID:31554687)
• The protease activity of human ATG4B is regulated by reversible oxidative modification. (PMID:31880198)
• MiR-449a attenuates autophagy of T-cell lymphoma cells by downregulating ATG4B expression. (PMID:32172731)
• Autophagy related 4B, upregulated by HIF-1alpha, attenuates the sensitivity to cisplatin in nasopharyngeal carcinoma cells. (PMID:32432742)
• Differential expression and prognostic relevance of autophagy-related markers ATG4B, GABARAP, and LC3B in breast cancer. (PMID:32685993)
• Distinct Mechanisms for Processing Autophagy Protein LC3-PE by RavZ and ATG4B. (PMID:32686895)
• PFKP facilitates ATG4B phosphorylation during amino acid deprivation-induced autophagy. (PMID:33607258)
• ATG4 family proteins drive phagophore growth independently of the LC3/GABARAP lipidation system. (PMID:33773106)
• ATG4B antagonizes antiviral immunity by GABARAP-directed autophagic degradation of TBK1. (PMID:37434364)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	atg4b	ENSDARG00000052104
mus_musculus	Atg4b	ENSMUSG00000026280
rattus_norvegicus	Atg4b	ENSRNOG00000018403
drosophila_melanogaster	Atg4a	FBGN0031298
caenorhabditis_elegans	atg-4.1	WBGENE00013595

Paralogs (3): ATG4A (ENSG00000101844), ATG4C (ENSG00000125703), ATG4D (ENSG00000130734)

Protein

Protein identifiers

Cysteine protease ATG4B — Q9Y4P1 (reviewed: Q9Y4P1)

Alternative names: AUT-like 1 cysteine endopeptidase, Autophagy-related cysteine endopeptidase 1, Autophagy-related protein 4 homolog B

All UniProt accessions (5): Q9Y4P1, C9J1C1, C9JIK8, F2Z2K8, H0Y2Y0

UniProt curated annotations — full annotation on UniProt →

Function. Cysteine protease that plays a key role in autophagy by mediating both proteolytic activation and delipidation of ATG8 family proteins. Required for canonical autophagy (macroautophagy), non-canonical autophagy as well as for mitophagy. The protease activity is required for proteolytic activation of ATG8 family proteins: cleaves the C-terminal amino acid of ATG8 proteins MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Protease activity is also required to counteract formation of high-molecular weight conjugates of ATG8 proteins (ATG8ylation): acts as a deubiquitinating-like enzyme that removes ATG8 conjugated to other proteins, such as ATG3. In addition to the protease activity, also mediates delipidation of ATG8 family proteins. Catalyzes delipidation of PE-conjugated forms of ATG8 proteins during macroautophagy. Also involved in non-canonical autophagy, a parallel pathway involving conjugation of ATG8 proteins to single membranes at endolysosomal compartments, by catalyzing delipidation of ATG8 proteins conjugated to phosphatidylserine (PS). Compared to other members of the family (ATG4A, ATG4C or ATG4C), constitutes the major protein for proteolytic activation of ATG8 proteins, while it displays weaker delipidation activity than other ATG4 paralogs. Involved in phagophore growth during mitophagy independently of its protease activity and of ATG8 proteins: acts by regulating ATG9A trafficking to mitochondria and promoting phagophore-endoplasmic reticulum contacts during the lipid transfer phase of mitophagy.

Subunit / interactions. Interacts with PFKP; promoting phosphorylation of ATG4B at Ser-34. Interacts with GBP7.

Subcellular location. Cytoplasm. Cytosol. Cytoplasmic vesicle. Autophagosome. Endoplasmic reticulum. Mitochondrion.

Post-translational modifications. Phosphorylation at Ser-383 and Ser-392 promotes autophagy by increasing protein delipidation activity without affecting proteolytic activation of ATG8 proteins. Phosphorylation at Ser-316 by ULK1 inhibits autophagy by decreasing both proteolytic activation and delipidation activities. Phosphorylation at Ser-316 is dephosphorylated by protein phosphatase 2A (PP2A). Phosphorylation at Ser-34 by AKT2 promotes its hydrolase activity, leading to increased proteolytic activation and delipidation of ATG8 family proteins. Phosphorylation at Ser-34 by AKT1 promotes mitochondrial localization and inhibition of the F1F0-ATP synthase activity, leading to elevation of mitochondrial reactive oxygen species (ROS). Ubiquitinated by RNF5, leading to its degradation by the proteasome. S-nitrosylation at Cys-189 and Cys-292 in response to high glucose decreases both proteolytic activation and delipidation activities. O-glycosylated by OGT, leading to increase protease activity, thereby promoting the proteolytic activation of ATG8 family proteins. Forms reversible intrachain disulfide bonds in response to oxidative stress. Forms interchain disulfide bonds, leading to formation of homooligomers in response to oxidation.

Activity regulation. Inhibited by N-ethylmaleimide. Redox-regulated during autophagy since reducing conditions activate ATG4A whereas an oxidizing environment such as the presence of H(2)O(2) inhibits its activity. The cysteine protease activity compounds is inhibited by styrylquinoline compounds 4-28 and LV-320.

Domain organisation. The LIR motif (LC3-interacting region) is required for the interaction with ATG8 family proteins MAP1LC3A, MAP1LC3B, MAP1LC3C and GABARAPL1. Required for proteolytic activation and delipidation of ATG8 proteins.

Similarity. Belongs to the peptidase C54 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9Y4P1-1	1	yes
Q9Y4P1-2	2
Q9Y4P1-3	3
Q9Y4P1-4	4
Q9Y4P1-6	6

RefSeq proteins (2): NP_037457, NP_847896 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005078	Peptidase_C54	Family
IPR038765	Papain-like_cys_pep_sf	Homologous_superfamily
IPR046792	Peptidase_C54_cat	Domain
IPR046793	ATG4_LIR	Conserved_site

Pfam: PF03416, PF20166

Catalyzed reactions (Rhea), 2 shown:

• [protein]-C-terminal L-amino acid-glycyl-phosphatidylethanolamide + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phosphoethanolamine (RHEA:67548)
• [protein]-C-terminal L-amino acid-glycyl-phosphatidylserine + H2O = [protein]-C-terminal L-amino acid-glycine + a 1,2-diacyl-sn-glycero-3-phospho-L-serine (RHEA:67576)

UniProt features (97 total): mutagenesis site 29, strand 20, helix 15, modified residue 8, splice variant 6, sequence conflict 5, turn 5, disulfide bond 3, active site 3, chain 1, short sequence motif 1, sequence variant 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
5LXI	X-RAY DIFFRACTION	1.44
5LXH	X-RAY DIFFRACTION	1.58
2CY7	X-RAY DIFFRACTION	1.9
2Z0D	X-RAY DIFFRACTION	1.9
2Z0E	X-RAY DIFFRACTION	1.9
2D1I	X-RAY DIFFRACTION	2
2ZZP	X-RAY DIFFRACTION	2.05

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y4P1-F1	86.74	0.71

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 (3): 74 (nucleophile); 278; 280

Post-translational modifications (8): 316, 383, 392, 1, 34, 189, 292, 301

Disulfide bonds (3): 292–361, 292, 361

Mutagenesis-validated functional residues (29):

Position	Phenotype
34	decreased phosphorylation by akt2, leading to reduced proteolytic activation of atg8 family proteins.
34	phospho-mimetic mutant; increased proteolytic activation of atg8 family proteins.
74	complete loss of protease activity.
78	reduces the redox sensitivity and retains activity in presence of h(2)o(2).
78	does not affect formation of disulfide bonds.
89	does not affect formation of disulfide bonds.
121	decreased phosphorylation by akt2; when associated with a-262.
142	strongly reduced protease activity.
183	does not affect formation of disulfide bonds.
189	does not affect s-nitrosylation. strongly decreased s-nitrosylation, leading to increased hydrolase activity and autopha
203	does not affect formation of disulfide bonds.
229	strongly reduced protease activity.
246	does not affect formation of disulfide bonds.
262	decreased phosphorylation by akt2; when associated with a-121.
278	complete loss of protease activity.
280	complete loss of protease activity.
292	does not affect s-nitrosylation. strongly decreased s-nitrosylation, leading to increased hydrolase activity and autopha
301	does not affect s-nitrosylation. does not affect formation of disulfide bonds.
306	does not affect formation of disulfide bonds.
316	abolished phosphorylation by ulk1; promotes hydrolase activity, leading to increased proteolytic activation and delipida
316	phospho-mimetic mutant; reduced hydrolase activity, leading to decreased proteolytic activation and delipidation of atg8
323	does not affect formation of disulfide bonds.
333	does not affect formation of disulfide bonds.
361	reduced formation of intrachain and interchain disulfide bonds in response to oxidation. abolished formation of disulfid
383	decreased phosphorylation, leading to decreased hydrolase activity and autophagic flux. does not affect interaction with

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1632852	Macroautophagy
R-HSA-9612973	Autophagy

MSigDB gene sets: 125 (showing top): GOBP_VACUOLE_ORGANIZATION, GCM_GSPT1, GOCC_VACUOLAR_MEMBRANE, GOBP_MACROAUTOPHAGY, GOBP_PROTEIN_MATURATION, GOBP_EAR_DEVELOPMENT, BLALOCK_ALZHEIMERS_DISEASE_UP, GOMF_CYSTEINE_TYPE_PEPTIDASE_ACTIVITY, GOBP_ORGANELLE_ASSEMBLY, MORF_EPHA7, GCM_NF2, GOBP_SENSORY_ORGAN_DEVELOPMENT, MORF_IL9, GOBP_AUTOPHAGOSOME_ORGANIZATION, MORF_DCC

GO Biological Process (13): autophagosome assembly (GO:0000045), mitophagy (GO:0000423), proteolysis (GO:0006508), autophagy (GO:0006914), protein transport (GO:0015031), macroautophagy (GO:0016236), microautophagy (GO:0016237), protein processing (GO:0016485), otolith mineralization completed early in development (GO:0031173), protein localization to phagophore assembly site (GO:0034497), piecemeal microautophagy of the nucleus (GO:0034727), aggrephagy (GO:0035973), protein delipidation (GO:0051697)

GO Molecular Function (8): endopeptidase activity (GO:0004175), cysteine-type endopeptidase activity (GO:0004197), cysteine-type peptidase activity (GO:0008234), protein-phosphatidylethanolamide deconjugating activity (GO:0019786), scaffold protein binding (GO:0097110), protein binding (GO:0005515), peptidase activity (GO:0008233), hydrolase activity (GO:0016787)

GO Cellular Component (7): autophagosome membrane (GO:0000421), cytoplasm (GO:0005737), mitochondrion (GO:0005739), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), cytoplasmic vesicle (GO:0031410), autophagosome (GO:0005776)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Autophagy	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
macroautophagy	2
intracellular protein localization	2
autophagosome assembly	2
autophagy	2
peptidase activity	2
hydrolase activity	2
catalytic activity, acting on a protein	2
cellular anatomical structure	2
intracellular membrane-bounded organelle	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
protein metabolic process	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
transport	1
establishment of protein localization	1
proteolysis	1
protein maturation	1
otolith mineralization	1
microautophagy	1
nucleophagy	1
nucleus disassembly	1
protein modification process	1
endopeptidase activity	1
cysteine-type peptidase activity	1
protein binding	1
binding	1
catalytic activity	1
vacuolar membrane	1
autophagosome	1
intracellular anatomical structure	1
endomembrane system	1

Protein interactions and networks

STRING

1822 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ATG4B	F5GZY7	F5GZY7	992
ATG4B	GABARAPL2	P60520	990
ATG4B	GABARAP	O95166	975
ATG4B	ATG7	O95352	972
ATG4B	ATG3	Q9NT62	955
ATG4B	MAP1LC3B	Q9GZQ8	949
ATG4B	MAP1LC3C	Q9BXW4	923
ATG4B	MAP1LC3A	Q9H492	912
ATG4B	ATG5	Q9H1Y0	905
ATG4B	ATG12	O94817	902
ATG4B	ATG10	Q9H0Y0	875
ATG4B	ATG16L1	Q676U5	841
ATG4B	BECN1	Q14457	823
ATG4B	ATG101	Q9BSB4	820
ATG4B	PIK3C3	Q8NEB9	794

IntAct

79 interactions, top by confidence:

A	B	Type	Score
MAP1LC3B	ATG4B	psi-mi:“MI:0915”(physical association)	0.950
ATG4B	MAP1LC3B	psi-mi:“MI:0407”(direct interaction)	0.950
MAP1LC3B	ATG4B	psi-mi:“MI:0194”(cleavage reaction)	0.950
GABARAPL2	ATG4B	psi-mi:“MI:0915”(physical association)	0.930
ATG4B	GABARAPL2	psi-mi:“MI:0407”(direct interaction)	0.930
ATG4B	GABARAPL2	psi-mi:“MI:0915”(physical association)	0.930
GABARAPL1	ATG4B	psi-mi:“MI:0915”(physical association)	0.830
ATG4B	GABARAPL1	psi-mi:“MI:0407”(direct interaction)	0.830
CSNK1D	PER2	psi-mi:“MI:0914”(association)	0.810
MAP1LC3B	ATG7	psi-mi:“MI:0914”(association)	0.740
ATG4B	GABARAP	psi-mi:“MI:0407”(direct interaction)	0.730
GABARAPL2	IPO5	psi-mi:“MI:0914”(association)	0.690
MAP1LC3C	ATG4B	psi-mi:“MI:0915”(physical association)	0.680
MAP1LC3C	ATG4B	psi-mi:“MI:0407”(direct interaction)	0.680
MAP1LC3A	ATG4B	psi-mi:“MI:0915”(physical association)	0.670
GABARAP	IPO5	psi-mi:“MI:0914”(association)	0.590
GABARAPL1	IPO5	psi-mi:“MI:0914”(association)	0.590
ULK1	ULK1	psi-mi:“MI:0914”(association)	0.560
ATG3	MAP1LC3B2	psi-mi:“MI:0914”(association)	0.530
STK3	PLK1	psi-mi:“MI:0914”(association)	0.530
STK16	FLG	psi-mi:“MI:0914”(association)	0.530
MAP1LC3B	NIPSNAP2	psi-mi:“MI:0914”(association)	0.520
ATG4B		psi-mi:“MI:0915”(physical association)	0.500
ATG8	ATG4B	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (175): ATG4B (Affinity Capture-RNA), ATG4B (Affinity Capture-RNA), ATG4B (Affinity Capture-RNA), MAP1LC3A (Biochemical Activity), GABARAPL2 (Biochemical Activity), GABARAPL1 (Biochemical Activity), MAP1LC3A (Biochemical Activity), GABARAPL1 (Biochemical Activity), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS), ATG4B (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2QC33, A0FKG7, A6H7H7, F1N9S8, O95453, P0C0T1, P42694, P50747, P69341, Q0IIH8, Q0VGM9, Q13572, Q28559, Q4R528, Q5BJZ6, Q5F480, Q5R699, Q5RC51, Q5ZIA0, Q5ZIW7, Q640G7, Q6DDJ3, Q6DFV5, Q6DG88, Q6DJB3, Q6GR37, Q6NYU2, Q6PZ02, Q6PZ03, Q6PZ05, Q7T0P6, Q80UY1, Q80YV4, Q811C2, Q8BGE6, Q8BYN3, Q8C9S8, Q8N4J0, Q8VDG3, Q8WYN0

Diamond homologs: A0A0G2QC33, A1CJ08, A2Q1V6, A2QY50, A2XHJ5, A6SDQ3, A7F045, A7KAL5, E2RDP2, K8ESC5, P0CQ10, P0CQ11, Q1E5M9, Q2HH40, Q2U5B0, Q2XPP4, Q4U3V5, Q523C3, Q5B7L0, Q5R699, Q5ZIW7, Q640G7, Q684M2, Q68FJ9, Q6CH28, Q6DG88, Q6GPU1, Q6PZ02, Q6PZ03, Q6PZ05, Q75KP8, Q7S3X7, Q7XPW8, Q86TL0, Q86ZL5, Q8BGE6, Q8BGV9, Q8C9S8, Q8S929, Q8WYN0

SIGNOR signaling

12 interactions.

A	Effect	B	Mechanism
ATG4B	up-regulates	MAP1LC3B	cleavage
ATG4B	“up-regulates activity”	MAP1LC3C	cleavage
PFKP	“up-regulates activity”	ATG4B	phosphorylation
AKT1	“up-regulates activity”	ATG4B	phosphorylation
AKT	“up-regulates activity”	ATG4B	phosphorylation
ATG4B	“down-regulates activity”	“ATP synthase”
STK26	“up-regulates activity”	ATG4B	phosphorylation
RNF5	“down-regulates quantity by destabilization”	ATG4B	ubiquitination
ULK1	“down-regulates activity”	ATG4B	phosphorylation
ATG4B	“up-regulates activity”	GABARAP	cleavage
ATG4B	“up-regulates activity”	GABARAPL2	cleavage

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 48 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	39.5×	2e-14
Autophagy	8	33.9×	9e-09

GO biological processes:

GO term	Partners	Fold	FDR
mitophagy	12	88.7×	8e-19
autophagosome assembly	14	73.2×	1e-20
autophagosome maturation	8	65.3×	3e-11
macroautophagy	6	33.6×	2e-06
cellular response to starvation	6	27.0×	6e-06
protein autophosphorylation	5	16.9×	6e-04
autophagy	5	12.8×	1e-03
protein phosphorylation	6	9.5×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	75
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1411455	NC_000002.11:g.(?238233417)(242801596_?)del	Pathogenic
442661	GRCh37/hg19 2q37.3(chr2:239748306-242783384)x1	Pathogenic
58914	GRCh38/hg38 2q37.3(chr2:241249295-242086301)x1	Pathogenic
814385	GRCh37/hg19 2q37.3(chr2:242340265-242783384)x1	Likely pathogenic

SpliceAI

3714 predictions. Top by Δscore:

Variant	Effect	Δscore
2:241637723:AGGT:A	donor_loss	1.0000
2:241637724:GG:G	donor_loss	1.0000
2:241637725:G:A	donor_loss	1.0000
2:241651008:A:AG	acceptor_gain	1.0000
2:241651009:G:GG	acceptor_gain	1.0000
2:241651009:GCT:G	acceptor_gain	1.0000
2:241651251:A:AG	acceptor_gain	1.0000
2:241651252:A:G	acceptor_gain	1.0000
2:241651255:A:AG	acceptor_gain	1.0000
2:241651256:A:G	acceptor_gain	1.0000
2:241653607:CGAGG:C	donor_loss	1.0000
2:241653609:AGG:A	donor_loss	1.0000
2:241653610:GGTG:G	donor_loss	1.0000
2:241653611:GTGA:G	donor_loss	1.0000
2:241653612:T:A	donor_loss	1.0000
2:241654543:TAG:T	acceptor_loss	1.0000
2:241654544:A:AG	acceptor_gain	1.0000
2:241654544:A:AT	acceptor_loss	1.0000
2:241654544:AGATT:A	acceptor_gain	1.0000
2:241654545:G:A	acceptor_loss	1.0000
2:241654545:G:GA	acceptor_gain	1.0000
2:241654545:GA:G	acceptor_gain	1.0000
2:241654545:GATT:G	acceptor_gain	1.0000
2:241654545:GATTG:G	acceptor_gain	1.0000
2:241654616:G:GT	donor_gain	1.0000
2:241654617:A:T	donor_gain	1.0000
2:241654620:G:GT	donor_gain	1.0000
2:241654621:A:T	donor_gain	1.0000
2:241654625:T:G	donor_gain	1.0000
2:241654644:A:G	donor_gain	1.0000

AlphaMissense

2596 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:241651315:G:C	R55T	1.000
2:241651315:G:T	R55M	1.000
2:241651316:G:C	R55S	1.000
2:241651316:G:T	R55S	1.000
2:241653532:G:C	D69H	1.000
2:241653541:T:A	W72R	1.000
2:241653541:T:C	W72R	1.000
2:241653543:G:C	W72C	1.000
2:241653543:G:T	W72C	1.000
2:241653544:G:C	G73R	1.000
2:241653545:G:A	G73D	1.000
2:241653547:T:C	C74R	1.000
2:241653561:T:G	C78W	1.000
2:241653563:G:A	G79E	1.000
2:241655279:G:A	G132R	1.000
2:241655279:G:C	G132R	1.000
2:241655280:G:A	G132E	1.000
2:241655309:T:A	W142R	1.000
2:241655309:T:C	W142R	1.000
2:241655311:G:C	W142C	1.000
2:241655311:G:T	W142C	1.000
2:241655316:G:A	G144E	1.000
2:241655319:C:A	P145H	1.000
2:241655331:C:A	A149D	1.000
2:241659170:T:A	V174D	1.000
2:241666798:G:A	G231E	1.000
2:241668180:G:A	G257E	1.000
2:241668183:G:A	G258E	1.000
2:241668198:C:A	A263D	1.000
2:241651311:T:C	Y54H	0.999

dbSNP variants (sampled 300 via entrez): RS1000003762 (2:241638313 A>G), RS1000051025 (2:241670166 A>C,G), RS1000113830 (2:241638565 C>A), RS1000188277 (2:241653676 G>A), RS1000276343 (2:241638430 C>G,T), RS1000289754 (2:241653446 C>A), RS1000336502 (2:241648665 T>C), RS1000343352 (2:241674021 C>G), RS1000420614 (2:241656970 C>A,T), RS1000438270 (2:241665971 A>T), RS1000493860 (2:241673032 TGTG>T), RS1000507855 (2:241647183 T>C,G), RS1000662698 (2:241642211 G>A,C), RS1000667755 (2:241652456 C>T), RS1000701168 (2:241662925 A>G)

Disease associations

OMIM: gene MIM:611338 | disease phenotypes: MIM:614213, MIM:614255, MIM:600721

GenCC curated gene-disease

Mondo (4): hereditary spastic paraplegia 30 (MONDO:0012476), neuropathy, hereditary sensory, type 2C (MONDO:0013634), intellectual disability, autosomal dominant 9 (MONDO:0013656), D-2-hydroxyglutaric aciduria 1 (MONDO:0024554)

Orphanet (4): Autosomal spastic paraplegia type 30 (Orphanet:101010), NESCAV syndrome (Orphanet:662367), D-2-hydroxyglutaric aciduria (Orphanet:79315), Hereditary sensory and autonomic neuropathy type 2 (Orphanet:970)

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001942_6	Prostate cancer	5.000000e-09
GCST003044_38	Crohn’s disease	1.000000e-09
GCST007436_13	Carotid intima media thickness	8.000000e-08
GCST008129_8	Body mass index	3.000000e-08
GCST009798_13	Asthma	5.000000e-36

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C563677	Spastic Paraplegia 30, Autosomal Recessive (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL1741221 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

7 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 132,947 (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
CHEMBL1200438	TIOCONAZOLE	4	15,162
CHEMBL277535	BIFONAZOLE	4	12,513
CHEMBL286494	HYPERICIN	3	16,266
CHEMBL51085	EBSELEN	3	13,237
CHEMBL121626	TOLFENAMIC ACID	2	20,424
CHEMBL473535	FENTICLOR	2	32,197
CHEMBL6246	ELLAGIC ACID	2	23,148

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — C54: Aut2 peptidase

Binding affinities (BindingDB)

294 measured of 310 human assays (332 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
6-bromanyl-2-(furan-2-yl)quinoline-4-carboxylic acid	IC50	23 nM
MLS000530403	IC50	58.8 nM
2-(benzoylcarbamothioylamino)-5,5-dimethyl-4,7-dihydrothieno[2,3-c]pyran-3-carboxylic acid	EC50	92 nM
4-chloranyl-N-(3,4-dihydro-2H-thiochromen-4-yl)-3-sulfamoyl-benzamide	IC50	121 nM
4-[2-(2-cyclohexyl-5,6-dimethylthieno[2,3-d]pyrimidin-4-yl)sulfanylacetyl]-1,3-dihydroquinoxalin-2-one	IC50	316 nM
7-Ethyl-5-(4-nitro-phenyl)-2-phenyl-3H-benzo[e][1,2,4]triazepine	IC50	399 nM
SMR000255593	IC50	502 nM
4-[(E)-[3-(2-methylanilino)-4-oxo-1-naphthalenylidene]amino]sulfonylbenzoic acid	IC50	522 nM
4-[(2,5-dichlorophenoxy)methyl]-N-[3,5-dimethyl-1-[(2,3,4,5,6-pentafluorophenyl)methyl]-4-pyrazolyl]benzamide	IC50	532 nM
SMR000200958	IC50	870 nM
4-({(4Z)-1-oxo-4-[(phenylsulfonyl)imino]-1,4-dihydronaphthalen-2-yl}amino)benzoic acid	IC50	967 nM
2-[(2-fluorobenzyl)thio]-5-(4-methylphenyl)-1,3,4-oxadiazole	EC50	1140 nM
SMR000516584	IC50	1270 nM
1-ethyl-6-methyl-3-[(E)-2-phenylethenyl]pyrimido[5,4-e][1,2,4]triazine-5,7-dione	EC50	1440 nM
(4E)-4-(1,3-benzodioxol-5-ylhydrazinylidene)-5-imino-1-phenyl-3-pyrazolamine	EC50	1600 nM
1,3,6-Trimethyl-1H-pyrimido[5,4-e][1,2,4]triazine-5,7-dione	EC50	1610 nM
SMR000236924	IC50	1620 nM
3-[[(E)-(3-methyl-5-nitro-6-oxidanylidene-cyclohexa-2,4-dien-1-ylidene)methyl]amino]-2-(phenoxymethyl)quinazolin-4-one	IC50	1640 nM
1,6-dimethyl-3-propyl-pyrimido[5,4-e][1,2,4]triazine-5,7-dione	EC50	1770 nM
(1Z)-1-[[2-[4-(1H-imidazol-2-yl)phthalazin-1-yl]hydrazinyl]methylidene]naphthalen-2-one	EC50	1960 nM
MLS002608219	IC50	2020 nM
3-[[anilino(oxo)methyl]amino]-5-phenyl-2-thiophenecarboxylic acid ethyl ester	EC50	2160 nM
(6E)-2-(2-furanyl)-5-imino-6-[[1-(4-methoxyphenyl)-2-pyrrolyl]methylidene]-[1,3,4]thiadiazolo[3,2-a]pyrimidin-7-one	IC50	2270 nM
(E)-4-(1,3-benzothiazol-2-yl)-5-[4-(N-methylanilino)-3-nitro-phenyl]pent-4-enoic acid	IC50	2270 nM
4-[(3aR,4S,9bS)-8-[(4-methoxyphenyl)sulfamoyl]-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinolin-4-yl]benzoic acid	EC50	2280 nM
MLS000537883	IC50	2360 nM
2-[[5-[(4-chlorophenoxy)methyl]-4-(2-furanylmethyl)-1,2,4-triazol-3-yl]thio]-1-(2-fluorophenyl)ethanone	IC50	2360 nM
4-bromobenzoic acid [2-(3,5-dimethoxyphenyl)-4-oxo-3-quinazolinyl] ester	IC50	2510 nM
2-[4-(4-bromophenyl)-1,3-thiazol-2-yl]-4-(3-ethoxy-4-hydroxybenzylidene)-5-phenyl-2,4-dihydro-3H-pyrazol-3-one	IC50	2540 nM
2-chloranyl-4-[5-[(1-oxidanylidene-[1,3]thiazolo[3,2-a]benzimidazol-2-ylidene)methyl]furan-2-yl]benzoic acid	IC50	2890 nM
3-(4-Biphenyl-4-yl-thiazol-2-ylamino)-6,7-dimethoxy-3H-isobenzofuran-1-one	EC50	2980 nM
4-({4-[5-(2-methyl-3-phenyl-2-propen-1-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]butanoyl}amino)benzoic acid	EC50	2980 nM
4-[(5Z)-4-keto-5-[(E)-2-methyl-3-phenyl-prop-2-enylidene]-2-thioxo-thiazolidin-3-yl]benzoic acid	IC50	3090 nM
MLS000778639	IC50	3100 nM
1,8-bis(azanyl)-3,6-dipyrrolidin-1-yl-2,7-naphthyridine-4-carbonitrile	IC50	3170 nM
2-tert-butyl-9,10-anthraquinone	EC50	3190 nM
2-Methyl-8-morpholin-4-yl-5,6-dioxo-5,6-dihydro-quinoline-4-carboxylic acid methyl ester	IC50	3210 nM
SMR000678837	IC50	3350 nM
5-(3,5-dimethoxyphenyl)-N-(4-fluorobenzo[d]thiazol-2-yl)-1,3,4-oxadiazol-2-amine	IC50	3520 nM
4-[8-[(3-methoxyphenyl)sulfamoyl]-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinolin-4-yl]benzoic acid	EC50	3880 nM
(5Z)-5-[(6-methoxy-2-piperidin-1-ylquinolin-3-yl)methylidene]-2-sulfanylidene-1,3-thiazolidin-4-one	IC50	4240 nM
(6Z)-5-azanylidene-6-[[1-(4-ethylphenyl)pyrrol-2-yl]methylidene]-3-methylsulfonyl-[1,2,4]thiadiazolo[4,5-a]pyrimidin-7-one	IC50	4250 nM
3-(2-chlorophenyl)-N-(3-cyano-5,6-dihydro-4H-cyclopenta[b]thiophen-2-yl)-4,5-dihydro-1,2-oxazole-5-carboxamide	IC50	4360 nM
MLS000584739	IC50	4380 nM
SMR000558865	IC50	4410 nM
(6E)-6-[(1,3-benzodioxol-5-ylamino)methylidene]-2,4-dibromocyclohexa-2,4-dien-1-one	IC50	4430 nM
MLS000762704	IC50	5080 nM
2-[(5-ethanoyl-2-ethoxy-phenyl)methylsulfanyl]-3-prop-2-enyl-quinazolin-4-one	IC50	5100 nM
(7-chloro-4-quinolyl)-[(2-methylbenzylidene)amino]amine	IC50	5130 nM
SMR000230796	IC50	5150 nM

ChEMBL bioactivities

237 potent at pChembl≥5 of 479 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.82	IC50	15	nM	CHEMBL4581663
7.24	IC50	57	nM	CHEMBL4581663
7.22	IC50	60	nM	CHEMBL4546760
7.14	IC50	73	nM	CHEMBL4520267
7.10	IC50	80	nM	CHEMBL4520267
6.96	IC50	110	nM	CHEMBL4546760
6.89	IC50	130	nM	CHEMBL4520585
6.79	IC50	162.8	nM	CHEMBL4520267
6.75	IC50	180	nM	EBSELEN
6.72	IC50	190	nM	CHEMBL4553669
6.72	IC50	189	nM	EBSELEN
6.68	IC50	210	nM	CHEMBL4520585
6.64	IC50	230	nM	CHEMBL4553669
6.57	IC50	270	nM	CHEMBL4567870
6.50	IC50	316	nM	CHEMBL1496397
6.44	IC50	360	nM	CHEMBL4469737
6.44	IC50	360	nM	CHEMBL4520267
6.40	IC50	399	nM	CHEMBL1391013
6.30	IC50	502	nM	CHEMBL1538079
6.28	IC50	530	nM	CHEMBL4567870
6.27	IC50	532	nM	CHEMBL1427626
6.21	IC50	610	nM	CHEMBL4560825
6.20	IC50	630	nM	CHEMBL303579
6.19	IC50	640	nM	CHEMBL4534968
6.18	IC50	653	nM	CHEMBL599924
6.14	IC50	720	nM	CHEMBL4578571
6.14	IC50	730	nM	CHEMBL4483776
6.07	IC50	850	nM	CHEMBL4575072
6.06	IC50	880	nM	CHEMBL4592322
6.06	IC50	870	nM	CHEMBL1494802
6.04	IC50	920	nM	CHEMBL4574173
6.02	IC50	950	nM	CHEMBL4579064
6.02	IC50	950	nM	CHEMBL4555963
6.00	IC50	1000	nM	CHEMBL4579064
6.00	IC50	1010	nM	CHEMBL4588146
6.00	IC50	1000	nM	CHEMBL4542508
5.98	IC50	1040	nM	CHEMBL4535723
5.97	IC50	1080	nM	CHEMBL4567655
5.96	IC50	1100	nM	CHEMBL4539211
5.96	IC50	1100	nM	CHEMBL4554555
5.96	IC50	1100	nM	CHEMBL4566626
5.95	IC50	1130	nM	CHEMBL4572200
5.92	IC50	1190	nM	CHEMBL4567655
5.92	IC50	1210	nM	CHEMBL4590201
5.92	IC50	1200	nM	CHEMBL4572200
5.90	IC50	1270	nM	CHEMBL4588146
5.90	IC50	1250	nM	9,10-PHENANTHRENEQUINONE
5.89	IC50	1300	nM	AURINTRICARBOXYLIC ACID
5.89	IC50	1300	nM	CHEMBL4576896
5.89	IC50	1300	nM	CHEMBL4579265

PubChem BioAssay actives

70 with measured affinity, of 564 total; 38 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-fluoro-N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]naphthalene-1-carboxamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.0150	uM
4-fluoro-N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]naphthalene-1-carboxamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.0600	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]naphthalene-1-carboxamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.0730	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)-methylamino]-1-oxo-3-phenylpropan-2-yl]naphthalene-1-carboxamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.1300	uM
2-phenyl-1,2-benzoselenazol-3-one	2074077: Inhibition of ATG4B (unknown origin) using pim-FG-PABA-AMC as substrate by fluorescence based assay	ic50	0.1800	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]cinnoline-4-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	0.1900	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]quinoline-4-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	0.2700	uM
4-[2-(2-cyclohexyl-5,6-dimethylthieno[2,3-d]pyrimidin-4-yl)sulfanylacetyl]-1,3-dihydroquinoxalin-2-one	1330870: Inhibition of wild type recombinant Atg4B (unknown origin) expressed in Escherichia coli BL21 DE3 using N-terminal His6-tagged LC3B-PLA2 as substrate after 60 mins by NBD-C6-HPC dye-based fluorescence assay	ic50	0.3160	uM
naphthalen-1-ylmethyl N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]carbamate	1607790: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	0.3600	uM
benzyl N-[(2S)-4-chloro-3-oxo-1-phenylbutan-2-yl]carbamate	1330871: Inhibition of Atg4B (unknown origin) using YFP-LC3B-EmGFP as substrate after 40 mins by FRET-based assay	ic50	0.6300	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]-3-methoxybenzamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	0.7200	uM
(2S)-N-(3-fluoro-2-oxopropyl)-3-phenyl-2-[(2-phenylacetyl)amino]propanamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.9200	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]pyrazine-2-carboxamide	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	0.9500	uM
3-chloro-N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]benzamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.0100	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]-3-(trifluoromethyl)benzamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.0400	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]naphthalene-2-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.0800	uM
benzyl N-[(2S)-3-(3-chlorophenyl)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxopropan-2-yl]carbamate	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.1000	uM
benzyl N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]carbamate	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.1300	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]benzamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.2100	uM
5-[(3-carboxy-4-hydroxyphenyl)-(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methyl]-2-hydroxybenzoic acid	1330871: Inhibition of Atg4B (unknown origin) using YFP-LC3B-EmGFP as substrate after 40 mins by FRET-based assay	ic50	1.3000	uM
Tioconazole	2074077: Inhibition of ATG4B (unknown origin) using pim-FG-PABA-AMC as substrate by fluorescence based assay	ic50	1.3000	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]cyclopentanecarboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	1.8600	uM
tert-butyl N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]carbamate	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	2.0000	uM
3,4,5-trihydroxy-6-oxobenzo[7]annulene-8-carboxylic acid	1330870: Inhibition of wild type recombinant Atg4B (unknown origin) expressed in Escherichia coli BL21 DE3 using N-terminal His6-tagged LC3B-PLA2 as substrate after 60 mins by NBD-C6-HPC dye-based fluorescence assay	ic50	2.3000	uM
3,6,10,13-tetrahydroxy-2-oxatetracyclo[6.6.2.04,16.011,15]hexadeca-1(15),3,5,8(16),10,12-hexaene-7,14-dione	1915512: Inhibition of recombinant ATG4B (unknown origin) expressed in Escherichia coli BL21 using LC3B-PLA2 as substrate incubated for 30 to 60 mins by High-throughput screening assay	ic50	3.0000	uM
6,7,13,14-tetrahydroxy-2,9-dioxatetracyclo[6.6.2.04,16.011,15]hexadeca-1(15),4,6,8(16),11,13-hexaene-3,10-dione	1607787: Inhibition of recombinant ATG4B (unknown origin) expressed in Escherichia coli BL21(DE3) using LC3-PLA2 as substrate by fluoroscence based assay	ic50	3.0000	uM
N-[2,3-bis(furan-2-yl)quinoxalin-6-yl]azepane-1-carbothioamide	1952611: Inhibition of N-terminal His6/SUMO-tagged full length human ATG4B expressed in Escherichia coli BL21 (DE3) cells using His-LC3B-GST as substrate preincubated with enzyme for 1 hr followed by substrate addition for 1 hr by HTRF assay	ic50	3.0800	uM
(E)-4-oxo-4-(4-undecylphenyl)but-2-enoic acid	1904097: Inhibition of recombinant ATG4B (unknown origin) expressed in Escherichia coli BL21(DE3) pLysS cells assessed as inhibition constant using LC3-GST as substrate incubated for 3 hrs by coomassie brilliant blue staining based assay	ki	3.1000	uM
N-[3-(diethylamino)propyl]-10-azatetracyclo[7.7.1.02,7.013,17]heptadeca-1(16),2,4,6,9,11,13(17),14-octaene-12-carboxamide	1607792: Inhibition of ATG4B (unknown origin) using FRET-GABARAPL2 as substrate preincubated for 30 mins followed by substrate addition and measured after 30 mins by fluorescence based assay	ic50	3.2400	uM
N-[3-(diethylamino)propyl]-8-oxo-10-azatetracyclo[7.7.1.02,7.013,17]heptadeca-1(16),2,4,6,9,11,13(17),14-octaene-12-carboxamide	1915516: Inhibition of ATG4B (unknown origin) by FRET assay	ic50	3.2400	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]pyridazine-3-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	3.6100	uM
benzyl N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-3-(3-fluorophenyl)-1-oxopropan-2-yl]carbamate	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	4.1200	uM
(E)-4-(4-octadecylphenyl)-4-oxobut-2-enoic acid	1904097: Inhibition of recombinant ATG4B (unknown origin) expressed in Escherichia coli BL21(DE3) pLysS cells assessed as inhibition constant using LC3-GST as substrate incubated for 3 hrs by coomassie brilliant blue staining based assay	ki	4.6000	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]-2-methoxynaphthalene-1-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	4.7900	uM
benzyl N-[(2S)-1-[[(2S)-4-fluoro-3-oxobutan-2-yl]amino]-1-oxo-3-phenylpropan-2-yl]carbamate	1637672: Inhibition of ATG4B (unknown origin) expressed in HEK293T cells coexpressing HTRA4 and Actin-LC3B-dNGLuc after 24 hrs by luciferase release assay	ic50	5.0900	uM
N-[(2S)-1-[(3-fluoro-2-oxopropyl)amino]-1-oxo-3-phenylpropan-2-yl]quinoline-8-carboxamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	6.4800	uM
9,11,13,16,18,20-hexahydroxy-5,24-dimethyloctacyclo[13.11.1.12,10.03,8.04,25.019,27.021,26.014,28]octacosa-1(26),2,4(25),5,8,10,12,14(28),15(27),16,18,20,23-tridecaene-7,22-dione	1915514: Inhibition of ATG4B (unknown origin) using proLC3B as substrate by FRET-LC3 assay	ic50	8.9000	uM
(2S)-N-(3-fluoro-2-oxopropyl)-2-[(2-phenoxyacetyl)amino]-3-phenylpropanamide	1637670: Inhibition of ATG4B (unknown origin) using His-GATE-16-GST as substrate preincubated for 30 mins followed by substrate addition measured after 30 mins by TR-FRET assay	ic50	9.1300	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	increases abundance, increases expression, affects reaction	2
aristolochic acid I	increases expression	1
AZD3965	decreases reaction, increases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
arsenite	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
beta-methylcholine	affects expression	1
4-phenylbutyric acid	decreases expression, decreases reaction	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
demycarosyl-3D-digitoxosylmithramycin SK	increases expression, affects cotreatment	1
Acetaminophen	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Anisomycin	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases expression	1
Cadmium	increases abundance, increases expression, affects reaction	1
Curcumin	decreases expression, decreases reaction, affects binding, increases expression	1
Deoxyglucose	affects cotreatment, increases expression	1
Dieldrin	increases response to substance	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Glycine	affects reaction, increases expression	1

ChEMBL screening assays

63 unique, capped per target: 61 binding, 2 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1738670	Functional	PUBCHEM_BIOASSAY: Dose response confirmation of the uHTS fluorescent assay for identification of inhibitors of ATG4B. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID504462, AID504475]	PubChem BioAssay data set
CHEMBL3870644	Binding	Inhibition of human recombinant GST-tagged Atg4B expressed in Escherichia coli at 4 mM preincubated for 15 mins followed by LC3B-GST substrate addition after 6 mins by SDS-PAGE assay	Inhibitor screening and enzymatic activity determination for autophagy target Atg4B using a gel electrophoresis-based assay. — Eur J Med Chem

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1KL	Abcam HeLa ATG4B KO	Cancer cell line	Female
CVCL_SD98	HAP1 ATG4B (-) 1	Cancer cell line	Male
CVCL_SD99	HAP1 ATG4B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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