Entity Detail — Knowledge Graph Node
This page aggregates everything SciDEX knows about KDM5B: its mechanistic relationships (Knowledge Graph edges), hypotheses targeting it, analyses mentioning it, and supporting scientific papers. The interactive graph below shows its immediate neighbors. All content is AI-synthesized from peer-reviewed literature.
| Gene Symbol | KDM5B |
| Full Name | Lysine Demethylase 5B |
| Chromosome | 1q32.1 |
| Function | encodes a Jumonji C (JmjC) domain-containing histone demethylase that specifically removes di- and trimethyl marks from histone H3 lysine 4 (H3K4me2/3). |
| Amino Acids | 1544 aa |
| Pathways | Angiogenesis, Epigenetic |
| UniProt ID | [Q9UGL1](https://www.uniprot.org/uniprot/Q9UGL1) |
| Ensembl ID | ENSG00000117139 |
| GeneCards | KDM5B |
| Human Protein Atlas | KDM5B |
| JmjN + JmjC domains | Together form the catalytic core; JmjC contains the Fe(II) and α-ketoglutarate (2-OG) binding sites required for oxidative demethylation |
| ARID domain | An AT-rich interaction domain that binds DNA, providing sequence-specific targeting to CCGCCC motifs enriched at CpG island promoters |
| PHD fingers (3x) | PHD1 reads unmethylated H3K4 (product recognition), PHD2 and PHD3 bind H3K4me3 (substrate recognition), enabling allosteric activation upon engagement with trimethylated substrates |
| C5HC2 zinc finger | Mediates protein-protein interactions for complex formation |
| Promoter H3K4me3 removal | KDM5B demethylates H3K4me3 at promoters of non-neural genes during neuronal differentiation, enabling silencing of progenitor programs as neurons mature |
| Associated Diseases | neurodegeneration |
| Interactions | NPM1, RNA, AND |
| KG Connections | 22 knowledge graph edges |
| Databases | GeneCardsNCBI GeneHPASTRING |
Knowledge base pages for this entity
graph TD
KDM5B["<b>KDM5B</b>"]
Als{"Als"}
KDM5B -->|"contributes to"| Als
Ms{"Ms"}
KDM5B -->|"contributes to"| Ms
Lipid_Metabolism(["Lipid Metabolism"])
KDM5B -->|"contributes to"| Lipid_Metabolism
neurodegeneration["neurodegeneration"]
KDM5B -->|"implicated in"| neurodegeneration
CYP27A1["CYP27A1"]
CYP27A1 -->|"contributes to"| KDM5B
DDIT3["DDIT3"]
DDIT3 -->|"associated with"| KDM5B
style KDM5B fill:#1a3a4a,stroke:#4fc3f7,stroke-width:3px,color:#e0e0e0| Target | Relation | Type | Str |
|---|---|---|---|
| Als | contributes_to | disease | 0.65 |
| Ms | contributes_to | disease | 0.65 |
| Als | therapeutic_target | disease | 0.65 |
| Fibrosis | therapeutic_target | disease | 0.65 |
| ALS | activates | disease | 0.65 |
| Fibrosis | activates | disease | 0.65 |
| Heart Failure | activates | disease | 0.65 |
| NPM1 | activates | gene | 0.60 |
| Lipid Metabolism | contributes_to | pathway | 0.60 |
| RNA | therapeutic_target | gene | 0.60 |
| Epigenetic | activates | pathway | 0.60 |
| Macrophage | activates | cell_type | 0.60 |
| Angiogenesis | activates | pathway | 0.60 |
| Macrophage | expressed_in | cell_type | 0.55 |
| Cardiac | activates | disease | 0.50 |
| MACROPHAGES | activates | concept | 0.50 |
Hypotheses where this entity is a therapeutic target
| Hypothesis | Score | Disease | Analysis |
|---|---|---|---|
| No targeting hypotheses | |||
Scientific analyses that reference this entity
No analyses mention this entity
Scientific publications cited in analyses involving this entity
| Title & PMID | Authors | Journal | Year | Citations |
|---|---|---|---|---|
| No papers found | ||||