ALKBH5

Summary

ALKBH5 (alkB homolog 5, RNA demethylase, HGNC:25996) is a protein-coding gene on chromosome 17p11.2, encoding RNA demethylase ALKBH5 (Q6P6C2). Dioxygenase that specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes.

Enables mRNA N6-methyladenosine dioxygenase activity and molecular condensate scaffold activity. Involved in membraneless organelle assembly; post-transcriptional regulation of gene expression; and response to hypoxia. Acts upstream of or within regulation of mRNA export from nucleus and regulation of mRNA processing. Located in Golgi apparatus; cytosol; and nuclear speck. Is active in paraspeckles.

Source: NCBI Gene 54890 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 67 total — 15 pathogenic
• Phenotypes (HPO): 3
• Druggable target: yes — 3 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_017758

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25996
Approved symbol	ALKBH5
Name	alkB homolog 5, RNA demethylase
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20308
Ensembl gene	ENSG00000091542
Ensembl biotype	protein_coding
OMIM	613303
Entrez	54890

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000399138, ENST00000490106, ENST00000541285

RefSeq mRNA: 1 — MANE Select: NM_017758 NM_017758

CCDS: CCDS42272

Canonical transcript exons

ENST00000399138 — 4 exons

Exon	Start	End
ENSE00001981350	18183828	18185013
ENSE00003518684	18206815	18206970
ENSE00003531842	18208219	18209954
ENSE00003536974	18194955	18195035

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 99.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 65.8249 / max 282.6214, expressed in 1826 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
159792	30.4466	1818
159790	14.9491	1802
159793	13.7097	1796
159794	3.2223	1353
159788	1.8222	726
159798	0.7871	503
159791	0.4838	255
159799	0.2301	93
159789	0.1082	22
159787	0.0658	14

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	99.04	gold quality
left ventricle myocardium	UBERON:0006566	98.49	gold quality
cardiac muscle of right atrium	UBERON:0003379	98.20	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.07	gold quality
oviduct epithelium	UBERON:0004804	98.07	gold quality
gastrocnemius	UBERON:0001388	98.06	gold quality
muscle of leg	UBERON:0001383	97.89	gold quality
ileal mucosa	UBERON:0000331	97.86	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.81	gold quality
skeletal muscle tissue	UBERON:0001134	97.53	gold quality
quadriceps femoris	UBERON:0001377	97.53	gold quality
kidney epithelium	UBERON:0004819	97.41	gold quality
vastus lateralis	UBERON:0001379	97.33	gold quality
secondary oocyte	CL:0000655	97.29	gold quality
muscle tissue	UBERON:0002385	97.02	gold quality
heart left ventricle	UBERON:0002084	96.86	gold quality
right testis	UBERON:0004534	96.86	gold quality
cardiac ventricle	UBERON:0002082	96.82	gold quality
cardiac atrium	UBERON:0002081	96.75	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.75	gold quality
left testis	UBERON:0004533	96.75	gold quality
right atrium auricular region	UBERON:0006631	96.68	gold quality
testis	UBERON:0000473	96.65	gold quality
body of tongue	UBERON:0011876	96.65	gold quality
biceps brachii	UBERON:0001507	96.48	gold quality
fallopian tube	UBERON:0003889	96.48	gold quality
apex of heart	UBERON:0002098	96.31	gold quality
upper arm skin	UBERON:0004263	96.31	silver quality
heart	UBERON:0000948	96.27	gold quality
deltoid	UBERON:0001476	96.09	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	26.73
E-MTAB-7606	no	460.90
E-GEOD-93593	no	302.79
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting ALKBH5, 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-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-548AR-3P	99.85	71.26	3889

Literature-anchored findings (GeneRIF, showing 40)

• ALKBH5 may have a role in the regulation of cellular responses to hypoxia as a class of HIF-transcriptional target gene (PMID:21264265)
• ALKBH5 is a RNA demethylase and its action strongly suggests that the reversible methyladenosine modification has fundamental and broad functions in mammalian cells. (PMID:23177736)
• Modelling substrate into the active site of ALKBH5 reveals conserved residues important for recognition and demethylation mechanisms. (PMID:24489119)
• findings provide a structural basis for understanding the substrate recognition specificity of Alkbh5 and offer a foundation for selective drug design against AlkB members (PMID:24616105)
• Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation. (PMID:24778178)
• The ALKBH5 gene may play a role in conferring risk of MDD in the Chinese population. (PMID:26047305)
• HIF-dependent ALKBH5 expression mediates enrichment of BCSCs in the hypoxic tumor microenvironment (PMID:27001847)
• N(6)-Methyladenosine itself serves as a ‘conformational marker’, which induces different conformational outcomes in RNAs depending on sequence context. This critically impacts its interactions with several m6A-recognising proteins, including FTO and ALKBH5. (PMID:27156733)
• ALKBH5 knockdown in breast cancer cells significantly decreased metastasis from breast to lungs in immunodeficient mice (PMID:27590511)
• ALKBH5-FOXM1 pathway is critical for glioblastoma proliferation and tumorigenesis.ALKBH5 expression increases in glioblastoma stem-like cells and predicts poor survival in glioblastoma patients. (PMID:28344040)
• Overexpression of ALKBH5 in MIA-PaCa-2 and BxPC-3 cells, demonstrats that ALKBH5 could inhibit cell migration and invasion and ALKBH5 inhibits cell motility by demethylating and increasing expression of KCNK15- AS1. (PMID:30032148)
• ALKBH5 role in the cancer growth and progression.METTL14 and ALKBH5 determine the N6-methyladenosine of target genes by controlling each other’s expression and by inhibiting YTHDF3. (PMID:30306128)
• the structure and dynamics of human Alkbh5 in solution (PMID:30352661)
• main eraser of N6-methyladenosine modification in germ cell tumors (PMID:30903744)
• ALKBH5 is a tumor-promoting gene in epithelial ovarian cancer, which is involved in the mTOR pathway and BCL-2-Beclin1 complex. (PMID:30987661)
• The m6A demethylase ALKBH5 controls trophoblast invasion at the maternal-fetal interface by regulating the stability of CYR61 mRNA. (PMID:31281518)
• The authors demonstrated that the ALKBH5 and lncRNA NEAT1 were significantly overexpressed in GC and that high expression of NEAT1 and ALKBH5 was correlated with invasion and metastasis in gastric cancer cells. (PMID:31290116)
• ALKBH5 Holds Prognostic Values and Inhibits the Metastasis of Colon Cancer. (PMID:31506804)
• METTL3-mediated m6A methylation is found to be dynamically reversed by the demethylase ALKBH5. In summary, this study highlights the functional importance of METTL3 in osteogenic differentiation and METTL3 may serve as a promising molecular target in regenerative medicine, as well as in the field of bone tissue engineering. (PMID:31643040)
• ALKBH5 affects the proliferation and invasion of lung adenocarcinoma cells under IH by downregulating m(6)A modification on FOXM1 mRNA and by promoting FOXM1 expression. (PMID:31677788)
• BMP2 Modified by the m(6)A Demethylation Enzyme ALKBH5 in the Ossification of the Ligamentum Flavum Through the AKT Signaling Pathway. (PMID:31897529)
• ALKBH5 repressed TIMP3 mRNA stability and protein production. In conclusion, the present research confirmed the ALKBH5/TIMP3 pathway in the non small lung cancer (NSCLC) oncogenesis progress, providing a novel insight for the epitranscriptome and potential therapeutic target for NSCLC. (PMID:31927006)
• DDX3 modulates cisplatin resistance in OSCC through ALKBH5-mediated m(6)A-demethylation of FOXM1 and NANOG. (PMID:31974865)
• ALKBH5 gene polymorphisms and Wilms tumor risk in Chinese children: A five-center case-control study. (PMID:32091154)
• m(6)A demethylase ALKBH5 inhibits tumor growth and metastasis by reducing YTHDFs-mediated YAP expression and inhibiting miR-107/LATS2-mediated YAP activity in NSCLC. (PMID:32106857)
• RNA demethylase ALKBH5 promotes ovarian carcinogenesis in a simulated tumour microenvironment through stimulating NF-kappaB pathway. (PMID:32329191)
• RNA Demethylase ALKBH5 Selectively Promotes Tumorigenesis and Cancer Stem Cell Self-Renewal in Acute Myeloid Leukemia. (PMID:32402250)
• RNA demethylase ALKBH5 prevents pancreatic cancer progression by posttranscriptional activation of PER1 in an m6A-YTHDF2-dependent manner. (PMID:32429928)
• m(6) A demethylase ALKBH5 promotes proliferation of esophageal squamous cell carcinoma associated with poor prognosis. (PMID:32449584)
• The study of METTL14, ALKBH5, and YTHDF2 in peripheral blood mononuclear cells from systemic lupus erythematosus. (PMID:32583611)
• Decreased Peripheral Blood ALKBH5 Correlates with Markers of Autoimmune Response in Systemic Lupus Erythematosus. (PMID:32685056)
• ALKBH5 suppresses malignancy of hepatocellular carcinoma via m(6)A-guided epigenetic inhibition of LYPD1. (PMID:32772918)
• Decreased ALKBH5, FTO, and YTHDF2 in Peripheral Blood Are as Risk Factors for Rheumatoid Arthritis. (PMID:32884942)
• Novel Prognostic Implications of Methylated RNA and Demethylases in Resected HCC and Background Liver Tissue. (PMID:33288560)
• Oxidative demethylase ALKBH5 repairs DNA alkylation damage and protects against alkylation-induced toxicity. (PMID:33321288)
• [ALKBH5 suppresses migration and invasion of human trophoblast cells by inhibiting epithelial-mesenchymal transition]. (PMID:33380386)
• ALKBH5-mediated m(6)A demethylation of FOXM1 mRNA promotes progression of uveal melanoma. (PMID:33428593)
• ALKBH5 suppresses tumor progression via an m(6)A-dependent epigenetic silencing of pre-miR-181b-1/YAP signaling axis in osteosarcoma. (PMID:33431791)
• ALKBH5 regulates cardiomyocyte proliferation and heart regeneration by demethylating the mRNA of YTHDF1. (PMID:33456585)
• ALKBH5-mediated m6A demethylation of lncRNA RMRP plays an oncogenic role in lung adenocarcinoma. (PMID:33934179)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	alkbh5	ENSDARG00000063003
mus_musculus	Alkbh5	ENSMUSG00000042650
rattus_norvegicus	Alkbh5	ENSRNOG00000028341

Protein

Protein identifiers

RNA demethylase ALKBH5 — Q6P6C2 (reviewed: Q6P6C2)

Alternative names: Alkylated DNA repair protein alkB homolog 5, Alpha-ketoglutarate-dependent dioxygenase alkB homolog 5

All UniProt accessions (2): Q6P6C2, K7ER58

UniProt curated annotations — full annotation on UniProt →

Function. Dioxygenase that specifically demethylates N(6)-methyladenosine (m6A) RNA, the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Demethylates RNA by oxidative demethylation, which requires molecular oxygen, alpha-ketoglutarate and iron. Demethylation of m6A mRNA affects mRNA processing, translation and export. Can also demethylate N(6)-methyladenosine in single-stranded DNA (in vitro). Required for the late meiotic and haploid phases of spermatogenesis by mediating m6A demethylation in spermatocytes and round spermatids: m6A demethylation of target transcripts is required for correct splicing and the production of longer 3’-UTR mRNAs in male germ cells. Involved in paraspeckle assembly, a nuclear membraneless organelle, by undergoing liquid-liquid phase separation. Paraspeckle assembly is coupled with m6A demethylation of RNAs, such as NEAT1 non-coding RNA. Also acts as a negative regulator of T-cell development: inhibits gamma-delta T-cell proliferation via demethylation of JAG1 and NOTCH2 transcripts. Inhibits regulatory T-cell (Treg) recruitment by mediating demethylation and destabilization of CCL28 mRNAs.

Subunit / interactions. Monomer. Interacts with RBM33; promoting desumoylation by SENP1 and recruitment to N(6)-methyladenosine-containing mRNAs. Interacts (when acetylated by KAT8) with PSPC1; interaction facilitates recognition of N(6)-methyladenosine (m6A) mRNA. Interacts with DDX54; this interaction down-regulates the interferon antiviral response.

Subcellular location. Nucleus speckle. Nucleus. Nucleoplasm.

Tissue specificity. Widely expressed, with highest expression in lung, followed by testis, pancreas, spleen and ovary.

Post-translational modifications. Phosphorylated at Ser-87 and Ser-325 in response to reactive oxygen species (ROS), promoting sumoylation and inactivation. Acetylated by KAT8 at Lys-235, promoting interaction with PSPC1, thereby facilitating recognition of N(6)-methyladenosine (m6A) mRNA by ALKBH5. Deacetylated at Lys-235 by HDAC7. Sumoylated at Lys-86 and Lys-321 by PIAS4 following phosphorylation at Ser-87 and Ser-325 in response to reactive oxygen species (ROS), inhibiting the RNA demethylase activity. Desumoylated by SENP1; relieving RNA demethylase inhibition, leading to N(6)-methyladenosine-containing mRNAs demethylation. Ubiquitinated at Lys-57 via ‘Lys-48’-linked polyubiquitin chain, leading to its degradation by the proteasome. Deubiquitinated at Lys-57 by USP9X, promoting its stabilizazion.

Activity regulation. RNA demethylase activity is inhibited following sumoylation. Inhibition is relieved following desumoylation.

Cofactor. Binds 1 Fe(2+) ion per subunit.

Domain organisation. The C-terminal disordered region undergoes liquid-liquid phase separation (LLPS) for the formation of paraspeckle membraneless compartment.

Induction. By hypoxia, directly activated by HIF1A. Expression is regulated by PRMT7.

Similarity. Belongs to the alkB family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6P6C2-2	2	yes
Q6P6C2-1	1
Q6P6C2-3	3

RefSeq proteins (1): NP_060228* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027450	AlkB-like	Domain
IPR032860	ALKBH5	Family
IPR037151	AlkB-like_sf	Homologous_superfamily

Pfam: PF13532

Enzyme classification (BRENDA):

• EC 1.14.11.53 — mRNA N6-methyladenine demethylase (BRENDA: 6 organisms, 33 substrates, 22 inhibitors, 11 Km, 10 kcat entries)

Substrate kinetics (BRENDA)

9 substrates with measured Km, best-characterized 9. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
N3-METHYLTHYMINE IN SINGLE-STRANDED DNA	0.0009–0.0019	2
N3-METHYLURACIL IN SINGLE-STRANDED MRNA	0.0021–0.0085	2
2-OXOGLUTARATE	0.0025	1
5’-UACACUCGAUCUGG(M6A)CUAAAGCUGCUC-3’-BIOTIN	0.0002	1
CCCC(M6A)CCCCCCCCC	2.583	1
GA(M6A)CA	2.251	1
GCGG(M6A)CUCCAGAUG	1.755	1
GG(M6A)CU	2.334	1
N6-METHYLADENINE IN MRNA	0.0017	1

Catalyzed reactions (Rhea), 1 shown:

• an N(6)-methyladenosine in mRNA + 2-oxoglutarate + O2 = an adenosine in mRNA + formaldehyde + succinate + CO2 (RHEA:49520)

UniProt features (97 total): mutagenesis site 33, strand 15, modified residue 13, helix 9, binding site 8, cross-link 4, region of interest 3, splice variant 2, compositionally biased region 2, turn 2, initiator methionine 1, chain 1, disulfide bond 1, coiled-coil region 1, sequence conflict 1, active site 1

Structure

Experimental structures (PDB)

11 structures.

PDB	Method	Resolution (Å)
4O7X	X-RAY DIFFRACTION	1.78
4NRP	X-RAY DIFFRACTION	1.8
4O61	X-RAY DIFFRACTION	1.9
4NJ4	X-RAY DIFFRACTION	2.02
7V4G	X-RAY DIFFRACTION	2.1
7WKV	X-RAY DIFFRACTION	2.1
4NRM	X-RAY DIFFRACTION	2.17
4OCT	X-RAY DIFFRACTION	2.28
4NRO	X-RAY DIFFRACTION	2.3
4NRQ	X-RAY DIFFRACTION	2.5
7WL0	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P6C2-F1	72.65	0.47

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): 139

Ligand- & substrate-binding residues (8): 195; 204; 204; 206; 266; 266; 277; 193

Post-translational modifications (17): 2, 64, 69, 71, 87, 132, 235, 325, 359, 361, 371, 374, 384, 57, 86, 321, 328

Disulfide bonds (1): 230–267

Mutagenesis-validated functional residues (33):

Position	Phenotype
57	abolished ubiquitination and degradation by the proteasome.
64	does not affect sumoylation.
69	does not affect sumoylation.
86	decreased sumoylation. abolished sumoylation, leading to increased mrna demethylase activity; when associated with r-321
87	decreased phosphorylation and subsequent sumoylation.
116	does not affect sumoylation.
123	does not affect interaction with rbm3.
128	does not affect interaction with rbm3.
130	abolishes catalytic activity.
132	no effect on catalytic activity with n(6)-methyladenosine in single-stranded dna. strongly reduced interaction with rbm3
139	abolishes catalytic activity.
141	abolishes catalytic activity with n(6)-methyladenosine in single-stranded dna.
147	does not affect ubiquitination.
151	does not affect interaction with rbm3.
153	no effect on catalytic activity. strongly reduced interaction with rbm33, leading to decreased rna demethylase activity.
195	abolishes catalytic activity.
204	abolishes catalytic activity.
206	does not affect interaction with rbm3.
209–210	abolishes catalytic activity.
232–234	impaired catalytic activity.
235	mimics acetylation; promoting rna demethylase activity.
235	abolished acetylation by kat8; inhibiting rna demethylase activity.
265	strongly reduced interaction with rbm33, leading to decreased rna demethylase activity.
266	impaired catalytic activity.
267	does not affect interaction with rbm3.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-73943	Reversal of alkylation damage by DNA dioxygenases
R-HSA-73894	DNA Repair
R-HSA-73942	DNA Damage Reversal

MSigDB gene sets: 205 (showing top): GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, NKX25_02, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_MALE_GAMETE_GENERATION, MODULE_308, CHX10_01, GOBP_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, GOBP_TRANSLATION, CREB_Q4, GOBP_NUCLEAR_TRANSPORT, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_LEUKOCYTE_PROLIFERATION, GOBP_REGULATION_OF_NUCLEOCYTOPLASMIC_TRANSPORT, GOBP_REGULATION_OF_CATABOLIC_PROCESS

GO Biological Process (11): response to hypoxia (GO:0001666), mRNA processing (GO:0006397), regulation of translation (GO:0006417), spermatogenesis (GO:0007283), regulation of mRNA export from nucleus (GO:0010793), cell differentiation (GO:0030154), gamma-delta T cell proliferation (GO:0046630), regulation of mRNA processing (GO:0050684), mRNA destabilization (GO:0061157), membraneless organelle assembly (GO:0140694), regulation of mRNA stability (GO:0043488)

GO Molecular Function (8): RNA binding (GO:0003723), 2-oxoglutarate-dependent dioxygenase activity (GO:0016706), oxidative RNA demethylase activity (GO:0035515), metal ion binding (GO:0046872), molecular condensate scaffold activity (GO:0140693), mRNA N6-methyladenosine dioxygenase activity (GO:1990931), oxidoreductase activity (GO:0016491), dioxygenase activity (GO:0051213)

GO Cellular Component (6): nucleus (GO:0005634), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), cytosol (GO:0005829), nuclear speck (GO:0016607), paraspeckles (GO:0042382)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
DNA Damage Reversal	1
DNA Repair	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
cytoplasm	2
nuclear ribonucleoprotein granule	2
response to stress	1
response to decreased oxygen levels	1
RNA processing	1
mRNA metabolic process	1
translation	1
post-transcriptional regulation of gene expression	1
regulation of protein metabolic process	1
developmental process involved in reproduction	1
male gamete generation	1
mRNA export from nucleus	1
regulation of RNA export from nucleus	1
regulation of ribonucleoprotein complex localization	1
cellular developmental process	1
T cell proliferation	1
gamma-delta T cell activation	1
mRNA processing	1
regulation of mRNA metabolic process	1
negative regulation of gene expression	1
regulation of mRNA stability	1
RNA destabilization	1
positive regulation of mRNA catabolic process	1
organelle assembly	1
regulation of RNA stability	1
regulation of mRNA catabolic process	1
nucleic acid binding	1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	1
dioxygenase activity	1
2-oxoglutarate-dependent dioxygenase activity	1
demethylase activity	1
catalytic activity, acting on RNA	1
cation binding	1
protein-macromolecule adaptor activity	1
oxidative RNA demethylase activity	1
catalytic activity	1
oxidoreductase activity	1
nuclear lumen	1

Protein interactions and networks

STRING

1292 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ALKBH5	DDX46	Q7L014	981
ALKBH5	ALKBH1	Q13686	980
ALKBH5	FTO	Q9C0B1	969
ALKBH5	YTHDF1	Q9BYJ9	954
ALKBH5	METTL14	Q9HCE5	952
ALKBH5	WTAP	Q15007	935
ALKBH5	METTL3	Q86U44	919
ALKBH5	YTHDC2	Q9H6S0	918
ALKBH5	YTHDC1	Q96MU7	918
ALKBH5	YTHDF2	Q9Y5A9	904
ALKBH5	YTHDF3	Q7Z739	900
ALKBH5	VIRMA	Q69YN4	893
ALKBH5	FOXM1	Q08050	893
ALKBH5	ZC3H13	Q5T200	891
ALKBH5	RBM15	Q96T37	888

IntAct

27 interactions, top by confidence:

A	B	Type	Score
KPNA6	RNMT	psi-mi:“MI:0914”(association)	0.800
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
ALKBH5	PROCR	psi-mi:“MI:0915”(physical association)	0.400
THOC7	ALYREF	psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
CEP135	MCRIP1	psi-mi:“MI:0914”(association)	0.350
CEP135	WWP2	psi-mi:“MI:0914”(association)	0.350
CEP135	WDR91	psi-mi:“MI:0914”(association)	0.350
DDX39B	RBM33	psi-mi:“MI:0914”(association)	0.350
MINK1	FECH	psi-mi:“MI:0914”(association)	0.350
PRP4K	YTHDC1	psi-mi:“MI:0914”(association)	0.350
RBM8A	MCRIP1	psi-mi:“MI:0914”(association)	0.350
	POLRMT	psi-mi:“MI:0914”(association)	0.350
	SUPT5H	psi-mi:“MI:0914”(association)	0.350
EPB41L5	LIN7A	psi-mi:“MI:0914”(association)	0.350
SF3B1	RBM10	psi-mi:“MI:0914”(association)	0.350
LMNA	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
ARGLU1	PIAS2	psi-mi:“MI:2364”(proximity)	0.270
TAF15	SBNO1	psi-mi:“MI:2364”(proximity)	0.270
NPM1	SBNO1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (68): ALKBH5 (Affinity Capture-MS), ALKBH5 (Affinity Capture-MS), ALKBH5 (Affinity Capture-RNA), ALKBH5 (Affinity Capture-MS), ALKBH5 (Affinity Capture-MS), ALKBH5 (Proximity Label-MS), ALKBH5 (Proximity Label-MS), ALKBH5 (Affinity Capture-MS), ALKBH5 (Proximity Label-MS), PROCR (Proximity Label-MS), ALKBH5 (Affinity Capture-MS), ALKBH5 (Affinity Capture-MS), ALKBH5 (Affinity Capture-RNA), ALKBH5 (Affinity Capture-MS), ALKBH5 (Reconstituted Complex)

ESM2 similar proteins: A2AQW0, B9EJ86, D3ZKD3, E1BH29, E6ZGB4, O75151, O88974, P0CH95, P17863, P49140, P55265, Q08BA6, Q0VGY8, Q15047, Q3TSG4, Q3UWM4, Q4KUS2, Q50H33, Q5CD77, Q5R6Y9, Q62739, Q62768, Q63802, Q66JG8, Q69ZT9, Q6GPB5, Q6NRE7, Q6P6C2, Q6ZN16, Q6ZWB6, Q7Z699, Q80TJ7, Q8AYK6, Q8CGA2, Q8CID0, Q8K1N4, Q8K4S7, Q8N5Y2, Q8QGV2, Q924S8

Diamond homologs: D3ZKD3, E1BH29, Q08BA6, Q3TSG4, Q66JG8, Q6GPB5, Q6P6C2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 36 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
mRNA Splicing - Major Pathway	7	11.9×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
mRNA export from nucleus	5	41.1×	2e-05
RNA splicing	8	19.6×	2e-06
mRNA splicing, via spliceosome	6	15.3×	2e-04
mRNA processing	5	10.9×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	15
Likely pathogenic	0
Uncertain significance	40
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (15)

Variant ID	HGVS	Classification
146492	GRCh38/hg38 17p11.2(chr17:16734588-18333372)x1	Pathogenic
146600	GRCh38/hg38 17p11.2(chr17:17788412-18333372)x1	Pathogenic
153282	GRCh38/hg38 17p11.2(chr17:17067833-19019419)x1	Pathogenic
154395	GRCh38/hg38 17p11.2(chr17:18077127-18521388)x3	Pathogenic
154919	GRCh38/hg38 17p11.2(chr17:16734588-18834703)x1	Pathogenic
1703554	GRCh37/hg19 17p11.2(chr17:17579860-18469185)	Pathogenic
1808657	GRCh37/hg19 17p11.2(chr17:17103571-19331028)x3	Pathogenic
2671583	Single allele	Pathogenic
4796203	GRCh38/hg38 17p11.2(chr17:17048995-18400908)x1	Pathogenic
523258	GRCh37/hg19 17p11.2(chr17:16936603-18184130)	Pathogenic
57224	GRCh38/hg38 17p11.2(chr17:16879232-18970941)x3	Pathogenic
58694	GRCh38/hg38 17p11.2(chr17:17667721-18301995)x3	Pathogenic
60433	GRCh38/hg38 17p11.2(chr17:16117885-18362819)x1	Pathogenic
60439	GRCh38/hg38 17p11.2(chr17:16817557-18362819)x1	Pathogenic
60458	GRCh38/hg38 17p11.2(chr17:17150076-18415759)x1	Pathogenic

SpliceAI

500 predictions. Top by Δscore:

Variant	Effect	Δscore
17:18194950:TTCA:T	acceptor_loss	1.0000
17:18194951:TCA:T	acceptor_loss	1.0000
17:18194952:CAGTG:C	acceptor_loss	1.0000
17:18194953:A:AG	acceptor_gain	1.0000
17:18194953:AGT:A	acceptor_gain	1.0000
17:18194953:AGTG:A	acceptor_gain	1.0000
17:18194954:G:GC	acceptor_gain	1.0000
17:18194954:GT:G	acceptor_gain	1.0000
17:18194954:GTG:G	acceptor_gain	1.0000
17:18194954:GTGG:G	acceptor_gain	1.0000
17:18194954:GTGGA:G	acceptor_gain	1.0000
17:18195031:AGGAA:A	donor_gain	1.0000
17:18195032:GGAA:G	donor_gain	1.0000
17:18195032:GGAAG:G	donor_gain	1.0000
17:18195033:GAA:G	donor_gain	1.0000
17:18195033:GAAG:G	donor_gain	1.0000
17:18195034:AA:A	donor_gain	1.0000
17:18195035:AGTA:A	donor_loss	1.0000
17:18195036:G:GG	donor_gain	1.0000
17:18195037:T:A	donor_loss	1.0000
17:18206813:A:AG	acceptor_gain	1.0000
17:18206814:G:GG	acceptor_gain	1.0000
17:18206814:GGACA:G	acceptor_gain	1.0000
17:18206966:CACAG:C	donor_loss	1.0000
17:18206967:ACAGG:A	donor_loss	1.0000
17:18206968:CAGGT:C	donor_loss	1.0000
17:18206969:AGGTA:A	donor_loss	1.0000
17:18206970:GGTA:G	donor_loss	1.0000
17:18206971:G:C	donor_loss	1.0000
17:18206972:T:G	donor_loss	1.0000

AlphaMissense

2559 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:18184527:T:C	F95S	1.000
17:18184555:G:C	E104D	1.000
17:18184555:G:T	E104D	1.000
17:18184563:T:A	I107N	1.000
17:18184616:G:C	D125H	1.000
17:18184617:A:C	D125A	1.000
17:18184617:A:G	D125G	1.000
17:18184617:A:T	D125V	1.000
17:18184623:C:A	A127D	1.000
17:18184629:T:A	L129Q	1.000
17:18184629:T:C	L129P	1.000
17:18184631:C:A	R130S	1.000
17:18184631:C:G	R130G	1.000
17:18184631:C:T	R130C	1.000
17:18184632:G:A	R130H	1.000
17:18184632:G:C	R130P	1.000
17:18184637:A:C	K132Q	1.000
17:18184637:A:G	K132E	1.000
17:18184638:A:T	K132M	1.000
17:18184639:G:C	K132N	1.000
17:18184639:G:T	K132N	1.000
17:18184640:T:C	Y133H	1.000
17:18184640:T:G	Y133D	1.000
17:18184641:A:C	Y133S	1.000
17:18184643:T:C	F134L	1.000
17:18184643:T:G	F134V	1.000
17:18184644:T:C	F134S	1.000
17:18184644:T:G	F134C	1.000
17:18184645:C:A	F134L	1.000
17:18184645:C:G	F134L	1.000

dbSNP variants (sampled 300 via entrez): RS1000028473 (17:18203458 G>A), RS1000091629 (17:18203974 C>A), RS1000126381 (17:18209657 G>A), RS1000168103 (17:18192695 T>C), RS1000297008 (17:18188650 G>A,C,T), RS1000311392 (17:18183799 G>C,T), RS1000326765 (17:18209806 T>C), RS1000335495 (17:18183304 TCTC>T), RS1000407307 (17:18183948 C>A,T), RS1000425475 (17:18183487 G>A), RS1000516355 (17:18204815 A>G), RS1000567439 (17:18188400 G>A), RS1000651480 (17:18186691 T>TC), RS1000764257 (17:18193674 C>T), RS1000814474 (17:18182510 T>A,C)

Disease associations

OMIM: gene MIM:613303 | disease phenotypes: MIM:610883, MIM:160700

GenCC curated gene-disease

Mondo (6): Potocki-Lupski syndrome (MONDO:0012574), methemoglobinemia (MONDO:0001117), microcephaly (MONDO:0001149), myopia (MONDO:0001384), strabismus (MONDO:0003432), brachydactyly (MONDO:0021004)

Orphanet (1): 17p11.2 microduplication syndrome (Orphanet:1713)

HPO phenotypes

3 total (3 of 3 shown, HPO-id order):

HPO	Term
HP:0000252	Microcephaly
HP:0000545	Myopia
HP:0001156	Brachydactyly

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001762_847	Obesity-related traits	4.000000e-06
GCST90020025_1407	Waist-to-hip ratio adjusted for BMI	1.000000e-13
GCST90020027_453	Waist-hip index	5.000000e-14
GCST90020029_586	Waist circumference adjusted for body mass index	3.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004908	testosterone measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D059327	Brachydactyly	C05.660.585.262; C16.131.621.585.262
D008708	Methemoglobinemia	C15.378.619
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D009216	Myopia	C11.744.636
D013285	Strabismus	C10.292.562.887; C11.590.810

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3621037 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

3 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,129,868 (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
CHEMBL25336	BISANTRENE	3	85
CHEMBL576	SUCCINIC ACID	3	1,121,639
CHEMBL38434	BREQUINAR	2	8,144

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

Binding affinities (BindingDB)

1 measured of 2 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5203668	IC50	17200 nM

ChEMBL bioactivities

95 potent at pChembl≥5 of 173 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.68	IC50	21	nM	CHEMBL5203605
7.21	IC50	61	nM	CHEMBL5172537
6.85	IC50	140	nM	BISANTRENE
6.77	IC50	170	nM	CHEMBL6177732
6.70	IC50	200	nM	CHEMBL6177732
6.58	IC50	260	nM	CHEMBL6177732
6.55	IC50	280	nM	CHEMBL6177732
6.46	IC50	350	nM	CHEMBL6177732
6.40	IC50	396	nM	CHEMBL5205465
6.39	Ki	410	nM	CHEMBL6177732
6.38	IC50	421	nM	CHEMBL5175898
6.35	IC50	450	nM	CHEMBL6175770
6.32	IC50	480	nM	CHEMBL6177732
6.26	IC50	550	nM	CHEMBL6175770
6.25	IC50	559	nM	CHEMBL5186162
6.25	Kd	560	nM	CHEMBL6177732
6.24	IC50	580	nM	CHEMBL6177732
6.23	IC50	591	nM	CHEMBL5208142
6.19	Kd	650	nM	CHEMBL6177732
6.15	IC50	710	nM	BREQUINAR
6.14	IC50	727	nM	CHEMBL5180828
6.11	IC50	780	nM	CHEMBL6177732
6.08	IC50	840	nM	CHEMBL4752151
6.05	IC50	890	nM	CHEMBL5202184
6.04	IC50	920	nM	CHEMBL5188113
5.99	Kd	1030	nM	CHEMBL6177732
5.94	Kd	1140	nM	CHEMBL6177732
5.91	IC50	1240	nM	CHEMBL5282066
5.84	IC50	1430	nM	CHEMBL6177732
5.82	IC50	1500	nM	CHEMBL5597347
5.75	IC50	1790	nM	CHEMBL4753950
5.75	IC50	1800	nM	CHEMBL5169684
5.70	IC50	1980	nM	CHEMBL465179
5.64	IC50	2300	nM	CHEMBL5199622
5.63	IC50	2320	nM	CHEMBL6142381
5.60	IC50	2500	nM	CHEMBL5195274
5.60	IC50	2530	nM	CHEMBL6177732
5.58	IC50	2600	nM	CHEMBL5208226
5.58	Kd	2630	nM	CHEMBL6177732
5.56	IC50	2734	nM	CHEMBL5195733
5.55	Kd	2800	nM	CHEMBL6177732
5.54	IC50	2900	nM	CHEMBL1230640
5.53	IC50	2970	nM	CHEMBL5401284
5.52	IC50	3000	nM	CHEMBL5207866
5.48	IC50	3300	nM	CHEMBL5181285
5.47	IC50	3400	nM	CHEMBL5194680
5.47	IC50	3400	nM	CHEMBL6175770
5.42	IC50	3848	nM	CHEMBL6173540
5.40	IC50	3970	nM	CHEMBL6176289
5.39	IC50	4060	nM	CHEMBL5401284

PubChem BioAssay actives

54 with measured affinity, of 191 total; 43 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
3-oxo-2-[3-(trifluoromethyl)phenyl]-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.0210	uM
2-(4-bromo-3-methylphenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.0610	uM
N-[(E)-[10-[(E)-(4,5-dihydro-1H-imidazol-2-ylhydrazinylidene)methyl]anthracen-9-yl]methylideneamino]-4,5-dihydro-1H-imidazol-2-amine	2119508: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP based assay	ic50	0.1400	uM
2-[4-methyl-3-(trifluoromethyl)phenyl]-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.3960	uM
2-[4-bromo-3-(trifluoromethyl)phenyl]-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.4210	uM
2-(3-bromo-4-methylphenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.5590	uM
2-(4-bromophenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.5910	uM
6-fluoro-2-[4-(2-fluorophenyl)phenyl]-3-methylquinoline-4-carboxylic acid	2119508: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP based assay	ic50	0.7100	uM
2-(3-bromophenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.7270	uM
2-(1-hydroxy-2-oxo-2-phenylethyl)sulfanylacetic acid	1710111: Inhibition of ALKBH5 demethylase activity (unknown origin) assessed as increase in methylated 6A-RNA level incubated for 2 hrs by colorimetric analysis	ic50	0.8400	uM
2-(3,4-dimethylphenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	0.8900	uM
1-(6-methoxyquinolin-3-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	0.9200	uM
1,9-dimethylcarbazole	1926037: Inhibition of ALKBH5 (unknown origin)	ic50	1.2400	uM
2-benzyl-4-cyclopropyl-1,2,4-thiadiazolidine-3,5-dione	2119514: Inhibition of ALKBH5 (unknown origin)	ic50	1.5000	uM
4-(furan-2-ylmethylamino)diazinane-3,6-dione	1710111: Inhibition of ALKBH5 demethylase activity (unknown origin) assessed as increase in methylated 6A-RNA level incubated for 2 hrs by colorimetric analysis	ic50	1.7900	uM
2-[(2-nitrophenyl)sulfonylcarbamoyl]pyridine-4-carboxylic acid	1860809: Inhibition of human full length N-terminal His6-tagged ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) Rosetta cells	ic50	1.8000	uM
3-amino-6-chloro-N-(diaminomethylidene)-5-(dimethylamino)pyrazine-2-carboxamide	1926037: Inhibition of ALKBH5 (unknown origin)	ic50	1.9800	uM
1-(6-fluoro-1H-indol-3-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	2.3000	uM
1-(4-fluoro-1H-indol-3-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	2.5000	uM
N-[[3-(3-fluoropyrrolidin-1-yl)oxetan-3-yl]methyl]-1-(5-phenylfuran-2-yl)methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	2.6000	uM
2-(4-chlorophenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	2.7340	uM
8-hydroxyquinoline-5-carboxylic acid	1926063: Inhibition of human ALKBH5 (74 to 294 residues) expressed in Escherichia coli BL21(DE3) V2R-pRARE cells using biotin labeled m6A-ss-RNA with UACACUCGAUCUGG(m6A)CUAAAGCUGCUC sequence as substrate incubated for 1 hr by TopCount scintillation counting method	ic50	2.9000	uM
[4-(trifluoromethyl)phenyl]methyl 4-[6-(2,6-dihydroxy-3-nitrobenzoyl)pyrazolo[1,5-a]pyrimidin-2-yl]benzoate	2022917: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP assay	ic50	2.9700	uM
N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]-1-[4-(trifluoromethylsulfanyl)phenyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	3.0000	uM
1-(1H-indol-5-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	3.3000	uM
1-(5-phenylthiophen-2-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	3.4000	uM
2-[4-(methylsulfamoylmethyl)phenyl]-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	4.2530	uM
[4-(trifluoromethyl)phenyl]methyl 4-[6-(2-hydroxy-5-nitrobenzoyl)pyrazolo[1,5-a]pyrimidin-2-yl]benzoate	2022917: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP assay	ic50	4.6400	uM
2-(3-methylphenyl)-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	4.9440	uM
2-[4-[(2-fluorophenyl)methylsulfamoylmethyl]phenyl]-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	5.0380	uM
1-(2,3-dihydro-1,4-benzodioxin-6-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	5.9000	uM
1-(5-fluoro-1H-indol-3-yl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	6.6000	uM
2-[4-[(4-fluorophenyl)methylsulfamoylmethyl]phenyl]-3-oxo-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	6.6070	uM
3-oxo-2-(4-propan-2-ylphenyl)-1H-pyrazole-5-carboxylic acid	1860812: Inhibition of human recombinant ALKBH5 (66 to 292 residues) expressed in Escherichia coli BL21 (DE3) cells using FAM-labeled ssRNA (5’-CUCGAUACG(m^6A) UCCGGUCAAA-3’) as substrate incubated for 60 mins by fluorescence polarization assay	ic50	6.6150	uM
(E)-4-[2-[4-[3,5-dichloro-4-(2-nitroanilino)anilino]pyridine-3-carbonyl]hydrazinyl]-4-oxobut-2-enoic acid	1876797: Inhibition of ALKBH5 (unknown origin) demethylation activity	ic50	7.1300	uM
2-(2,4-dihydroxyphenyl)-3,5,7-trihydroxychromen-4-one	1926037: Inhibition of ALKBH5 (unknown origin)	ic50	7.1300	uM
benzyl 4-[6-(2-hydroxy-5-nitrobenzoyl)pyrazolo[1,5-a]pyrimidin-2-yl]benzoate	2022917: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP assay	ic50	7.8800	uM
(E)-4-[2-[4-[3,5-dichloro-2-methyl-4-(2-nitroanilino)anilino]pyridine-3-carbonyl]hydrazinyl]-4-oxobut-2-enoic acid	1876797: Inhibition of ALKBH5 (unknown origin) demethylation activity	ic50	8.9800	uM
4,5-dihydroxy-9,10-dioxoanthracene-2-carboxylic acid	2119503: Inhibition of ALKBH5 (unknown origin) expressed in Escherichia coli BL21 (DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3 as substrate pre-incubated for 30 mins followed by substrate addition and measured for 1 hrs by FP based analysis	ic50	9.0000	uM
methyl 4-[6-(2-hydroxy-5-nitrobenzoyl)pyrazolo[1,5-a]pyrimidin-2-yl]benzoate	2022917: Inhibition of ALKBH5 (66 to 292 residues)(unknown origin) expressed in Escherichia coli BL21(DE3) using 5’-ATTGTCA(m6A)CAGCAGA-FAM-3’ as substrate incubated for 30 mins by FP assay	ic50	9.1200	uM
pyridine-2,4-dicarboxylic acid	1926037: Inhibition of ALKBH5 (unknown origin)	ic50	9.4300	uM
1-(3,4-dimethylphenyl)-N-[(3-pyrrolidin-1-yloxetan-3-yl)methyl]methanamine	1886503: Inhibition of ALKBH5 (unknown origin)	ic50	9.9000	uM
2-methyl-3-propylimidazo[1,2-c][1,3]benzoxazine-5-thione	2119513: Inhibition of N-terminal ALKBH5 (unknown origin) expressed in Sf9 cells	ic50	10.0000	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases reaction, increases expression, decreases expression	4
bisphenol A	increases methylation, increases expression, affects expression, affects cotreatment	3
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
quinone	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
cobaltous chloride	increases expression	1
3-deazaadenosine	decreases expression, decreases reaction	1
thallium acetate	decreases reaction, affects reaction, increases expression, decreases expression	1
aflatoxin B2	increases methylation	1
coumarin	decreases phosphorylation	1
cadmium sulfate	increases abundance, decreases expression	1
fumonisin B1	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
eprenetapopt	affects expression, affects reaction	1
PKF115-584	affects cotreatment, decreases expression, increases reaction, increases expression	1
bisphenol S	increases methylation	1
(+)-JQ1 compound	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetylcysteine	decreases reaction, increases expression	1
Arsenic	increases expression	1
Cadmium	decreases expression, increases abundance	1
Caffeine	decreases phosphorylation	1
Cobalt	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	affects phosphorylation, affects response to substance	1
Formaldehyde	decreases expression	1
Methyl Methanesulfonate	decreases expression	1

ChEMBL screening assays

130 unique, capped per target: 130 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3626967	Binding	Inhibition of N-terminal His-tagged human recombinant ALKBH5 (66 to 292 residues) catalytic domain expressed in Escherichia coli BL21 assessed as reduction in 5-mer ssRNA (5’-GGm6ACU-3’) demethylation incubated for 6 mins by MALDI-TOF mass	Repair of methyl lesions in RNA by oxidative demethylation — Medchemcomm

Cellosaurus cell lines

7 cell lines: 4 cancer cell line, 3 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2RJ	Abcam HEK293T ALKBH5 KO	Transformed cell line	Female
CVCL_B8SC	Abcam MCF-7 ALKBH5 KO	Cancer cell line	Female
CVCL_C0U1	HEK293T ALKBH5/FTO DKO	Transformed cell line	Female
CVCL_D8Z2	Ubigene HEK293 ALKBH5 KO	Transformed cell line	Female
CVCL_E1Q6	HAP1 ALKBH5 (-) 1	Cancer cell line	Male
CVCL_E1Q7	HAP1 ALKBH5 (-) 2	Cancer cell line	Male
CVCL_E1Q8	HAP1 ALKBH5 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00347204	PHASE4	COMPLETED	Comparison of Acular LS Versus Nevanac for Pain Control in Eyes Undergoing PRK
NCT00349843	PHASE4	COMPLETED	Investigation of Multi-Purpose Solution-Based Corneal Staining and Ocular Comfort
NCT00349882	PHASE4	COMPLETED	Effects of Contact Lens Care Regimens on the Corneal Epithelium
NCT00350246	PHASE4	COMPLETED	Long-term Effects of Laser Refractive Surgery
NCT00404105	PHASE4	COMPLETED	A Comparison of PRK and LASIK for Correction of Myopia
NCT00455455	PHASE4	COMPLETED	Corneal and Conjunctival Sensitivity and Staining Study
NCT00541177	PHASE4	UNKNOWN	Study of Myopia Prevention in Children With Low Concentration of Atropine
NCT00627302	PHASE4	COMPLETED	Efficacy of PEG-400 and Systane Artificial Tears (Alcon) on Quality of Vision
NCT00640341	PHASE4	COMPLETED	Comparative Performance of PureVision, Acuvue Oasys and O2Optix
NCT00770094	PHASE4	UNKNOWN	Multi Laser Platform Comparison Study for LASIK
NCT00821236	PHASE4	COMPLETED	Contralateral Comparison of Three Excimer Laser Systems in Performing LASIK
NCT00889941	PHASE4	COMPLETED	Effect of Preoperative Pupil Size on Quality of Vision After Wavefront-Guided LASIK
NCT00937105	PHASE4	COMPLETED	Daily Wear Corneal Infiltrative Event Study
NCT01173198	PHASE4	COMPLETED	An Evaluation of Outcomes Following Wavefront Optimized or Wavefront Guided Lasik Procedure in Low to Moderate Myopic Patients
NCT01250925	PHASE4	COMPLETED	Effect of Contact Lens Wear on Immune Cell Density and Morphology of the Ocular Surface
NCT01387360	PHASE4	COMPLETED	Presbyopic Supracor Treatment for Near Myopic/Hyperopic Pseudophakic Eyes
NCT01454843	PHASE4	COMPLETED	LASIK Using the Alcon Allegretto Wavefront-Guided Excimer Laser vs AMO Visx Wavefront-Guided Excimer Laser
NCT01693939	PHASE4	COMPLETED	Evaluation of the Post-LASIK Flap Thickness of the FS200 Femtosecond Laser Flap
NCT01706237	PHASE4	WITHDRAWN	Visual Outcomes And Contrast Sensitivity After Myopic Wavefront-Optimized Lasik With Nexisvision Shield Or Bandage Contact Lens
NCT01746589	PHASE4	COMPLETED	Visual Outcomes and Contrast Sensitivity After Myopic LASIK
NCT01977807	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser in Asian Eyes Using LASIK
NCT02071576	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of the 500 Hz Technolas Perfect Vision Excimer Laser Using LASIK
NCT02112968	PHASE4	UNKNOWN	A Prospective Safety and Effectiveness Study of a New High Repetition Rate Excimer Laser Using LASIK for the Correction of Ammetropia and Presbyopia
NCT02186184	PHASE4	COMPLETED	Effect of Orthokeratology Versus Spectacles on Myopia Progression in Chinese Children: A Crossover Trial
NCT02544529	PHASE4	WITHDRAWN	Echothiophate Iodide for the Prevention of Progression of Myopia
NCT03001401	PHASE4	UNKNOWN	Comparison of Next Generation Laser Techniques of Myopia Correction: iDesign vs. SMILE
NCT03158142	PHASE4	COMPLETED	The Influence of Atropine on Choroidal Thickness
NCT03544827	PHASE4	COMPLETED	The Effects of Low Dose Atropine on Choroidal Thickness
NCT03881670	PHASE4	COMPLETED	On-Eye Optical Quality of Lotrafilcon B Lenses Over 12 Hours
NCT03949101	PHASE4	UNKNOWN	Atropine for Children and Adolescent Myopia Progression Study
NCT04208750	PHASE4	COMPLETED	Clinical Investigation of the Vision-R800 Device.
NCT04283331	PHASE4	UNKNOWN	Anesthetic Impregnated Bandage Soft Contact Lens (BSCL) in Pain Management After Photorefractive Keratectomy (PRK)
NCT05357326	PHASE4	UNKNOWN	Myopia Intervention in Children and Adolescents and Establishment of a Precise Intervention Model
NCT05448989	PHASE4	UNKNOWN	Efficacy and Safety of 1% Atropine 5+3 Regimen in Children and Adolescents Controlling Myopia
NCT05449015	PHASE4	UNKNOWN	Study on the Effect of Two Ways of Cycloplegia on Biological Parameters of Ciliary Muscle
NCT05733741	PHASE4	COMPLETED	Preservative-free Topical Anesthetics for Post-PRK Pain
NCT05803863	PHASE4	UNKNOWN	Efficacy Comparison of 2 Low-dose Atropine Eye Drops in Vietnamese Children Myopia Management
NCT06431841	PHASE4	ACTIVE_NOT_RECRUITING	Atropine and Spectacle Combination Treatment (ASPECT): 12-month Results of a Randomized Clinical Trial for Myopia Control
NCT06450132	PHASE4	ACTIVE_NOT_RECRUITING	Changes in Eye Shape With Myopia Management Interventions
NCT06553404	PHASE4	ACTIVE_NOT_RECRUITING	Myoslow Lens Study to Control Myopia in Children