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Tchem
SMYD3
Histone-lysine N-methyltransferase SMYD3

Protein Summary
Description
Histone methyltransferase. Specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation (PubMed:15235609, PubMed:22419068). Also methylates 'Lys-5' of histone H4 (PubMed:22419068). Plays an important role in transcriptional activation as a member of an RNA polymerase complex (PubMed:15235609). Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences (PubMed:15235609). This gene encodes a histone methyltransferase which functions in RNA polymerase II complexes by an interaction with a specific RNA helicase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000490107
  • ENSP00000419184
  • ENSG00000185420
  • ENST00000630181
  • ENSP00000487434

Symbol
  • ZMYND1
  • ZNFN3A1
  • KMT3E
  • ZMYND1
  • ZNFN3A1
  • bA74P14.1
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
molecular function
0.99
trait
0.97
biological process
0.94
virus perturbation
0.88
transcription factor binding site profile
0.81


Related Tools
Target Illumination GWAS Analytics (TIGA)
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TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.
GENEVA
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GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.
GlyGen
Thumbnail image for GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
IDG Development Level Summary
Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 129.48   (req: < 5)
Gene RIFs: 62   (req: <= 3)
Antibodies: 251   (req: <= 50)
Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 129.48   (req: >= 5)
Gene RIFs: 62   (req: > 3)
Antibodies: 251   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 12
Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligands: 79
Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0
Active Ligands (79)
1 – 10 of 79
CHEMBL3798006
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CHEMBL3797749
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CHEMBL3797708
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CHEMBL3798741
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CHEMBL3798468
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CHEMBL4594207
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CHEMBL4573978
Rendered image for CHEMBL4573978
CHEMBL3797949
Rendered image for CHEMBL3797949
CHEMBL3798012
Rendered image for CHEMBL3798012
CHEMBL4521928
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GWAS Traits (6)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
lymphocyte count
1
1
1
57.8
lymphocyte percentage of leukocytes
1
1
1
35
electrocardiography
1
1
3
33.1
Cognitive impairment
1
1
0
1.5
21.5
hemolysis
1
1
0
21.2
15.8
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
lymphocyte count
1
57.8
lymphocyte percentage of leukocytes
1
35
electrocardiography
3
33.1
Cognitive impairment
0
1.5
21.5
hemolysis
0
21.2
15.8
Orthologs (4)
1 – 4 of 4
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Macaque
SET and MYND domain containing 3
703402
Mouse
MGI:1916976
69726
Cow
SET and MYND domain containing 3
VGNC:35044
616050
Zebrafish
ZDB-GENE-051120-138
569507
Species
Name
OMA
EggNOG
Inparanoid
Macaque
SET and MYND domain containing 3
Mouse
Cow
SET and MYND domain containing 3
Zebrafish
Protein Structure (15 Structures, 1 AlphaFold Model)
RepresentationColor Scheme

Click on a row in the table to change the structure displayed.
More information can be found at RCSB PDB

AF-Q9H7B4-F1-model_v1

AlphaFold Structures Developed by DeepMind and EMBL-EBI

1 – 5 of 15
PDB Structure Id
Ligand
Method
Resolution (Å)
Residues
Fraction of Total Protein
Pub Year
Title
PDB Structure Id
Fraction of Total Protein
Resolution
Pub Year
Pathways (4)
Chromatin modifying enzymes (R-HSA-3247509)

Click on a row in the table to change the structure displayed.

Items per page:
1 – 3 of 3
Data Source
Name
Explore in Pharos
Explore in Source
Reactome
Chromatin modifying enzymes
Reactome
Chromatin organization
Reactome
PKMTs methylate histone lysines
Name
Explore in Pharos
Explore in Source
Chromatin modifying enzymes
Chromatin organization
PKMTs methylate histone lysines
Gene Ontology Terms (15)
Items per page:
10
1 – 5 of 5
GO Term
Evidence
Assigned by
Inferred from Mutant Phenotype (IMP)
UniProtKB
Inferred from Electronic Annotation (IEA)
UniProtKB-KW
Inferred from Electronic Annotation (IEA)
Ensembl
Inferred from Electronic Annotation (IEA)
Ensembl
Inferred from Electronic Annotation (IEA)
Ensembl
Protein-Protein Interactions (104)
1 – 10 of 104
HSP90AB3P
Tdark
p_int:  0.999999829
p_ni:  1.7e-7
p_wrong:  1e-9
Data Source:  BioPlex
HSP90AB4P
Tdark
p_int:  0.999999635
p_ni:  3.65e-7
Data Source:  BioPlex
HSP90AA5P
Tdark
p_int:  0.999975728
p_ni:  0.000024251
p_wrong:  2e-8
Data Source:  BioPlex
RCAN3
Tbio
Novelty:  0.12819457
p_int:  0.9960711
p_ni:  0.003548159
p_wrong:  0.000380741
Score:  0.207
Data Source:  BioPlex,STRINGDB
HSP90AA1
Tchem
Novelty:  0.00016774
p_int:  0.994797126
p_ni:  0.005202874
Score:  0.709
Data Source:  BioPlex,STRINGDB
HSP90AB1
Tchem
Novelty:  0.00907961
p_int:  0.991392809
p_ni:  0.008607191
Score:  0.486
Data Source:  BioPlex,STRINGDB
KDM3B
Tbio
Family:  Epigenetic
Novelty:  0.05322289
p_int:  0.958719081
p_ni:  0.041009623
p_wrong:  0.000271295
Score:  0.617
Data Source:  BioPlex,STRINGDB
MAP3K2
Tchem
Family:  Kinase
Novelty:  0.01201472
Score:  0.939
Data Source:  STRINGDB
HELZ
Tbio
Family:  Enzyme
Novelty:  0.08786982
Score:  0.879
Data Source:  STRINGDB
EZH2
Tclin
Family:  Epigenetic
Novelty:  0.00052816
Score:  0.851
Data Source:  STRINGDB
Publication Statistics
PubMed Score  129.48

PubMed score by year
PubTator Score  64.63

PubTator score by year
Amino Acid Sequence
Residue Counts
Protein Sequence
ProtVista Viewer
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