Tclin VDR Vitamin D3 receptor

Protein Classes

PANTHER Classes

Protein / Transcription Factor / Vitamin D3 Receptor

Protein / Receptor / Vitamin D3 Receptor

Protein / Nucleic Acid Binding / Vitamin D3 Receptor

Protein / ... / C4 Zinc Finger Nuclear Receptor / Vitamin D3 Receptor

DTO Classes

Protein / Nuclear Receptor / Vitamin D Receptor-like Receptors / Vitamin D3 Receptor

Protein Summary

Description

Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (PubMed:28698609, PubMed:16913708, PubMed:15728261, PubMed:10678179). Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR (PubMed:28698609). The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target genes (PubMed:28698609). Plays a central role in calcium homeostasis (By similarity). This gene encodes vitamin D3 receptor, which is a member of the nuclear hormone receptor superfamily of ligand-inducible transcription factors. This receptor also functions as a receptor for the secondary bile acid, lithocholic acid. Downstream targets of vitamin D3 receptor are principally involved in mineral metabolism, though this receptor regulates a variety of other metabolic pathways, such as those involved in immune response and cancer. Mutations in this gene are associated with type II vitamin D-resistant rickets. A single nucleotide polymorphism in the initiation codon results in an alternate translation start site three codons downstream. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Jun 2018]

Uniprot Accession IDs

• P11473
• B2R5Q1
• G3V1V9
• Q5PSV3
• VDR

Gene Name

• VDR

Ensembl ID

• ENST00000229022
• ENSP00000229022
• ENSG00000111424
• ENST00000395324
• ENSP00000378734
• ENST00000549336
• ENSP00000449573
• ENST00000550325
• ENSP00000447173

Symbol

• NR1I1
• NR1I1
• PPP1R163

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
molecular function	1
biological process	0.99
virus perturbation	0.98
hub protein	0.97
chemical	0.95

Related Tools

Target Illumination GWAS Analytics (TIGA)

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GENEVA

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.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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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: 1240.33   (req: < 5)

Gene RIFs: 1346   (req: <= 3)

Antibodies: 722   (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: 1240.33   (req: >= 5)

Gene RIFs: 1346   (req: > 3)

Antibodies: 722   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 41

Tchem

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

Active Ligands: 101

Tclin

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

Active Drugs: 9

Approved Drugs (9)

Explore Approved Drugs

1 – 9 of 9

colecalciferol

VDRTclin NR

AGONIST EC50 : 9.68

calcitriol

VDRTclin NR

AGONIST EC50 : 8.4

alfacalcidol

VDRTclin NR

AGONIST :

ergocalciferol

VDRTclin NR

AGONIST :

paricalcitol

VDRTclin NR

AGONIST EC50 : 8.7

doxercalciferol

VDRTclin NR

AGONIST :

calcifediol

VDRTclin NR

AGONIST :

calcipotriene

VDRTclin NR

AGONIST Kd : 9.51

eldecalcitol

VDRTclin NR

AGONIST :

Active Ligands (101)

Explore Active Ligands

1 – 10 of 101

CHEMBL1478

VDRTclin NR

: 5.1

CHEMBL1164992

VDRTclin NR

IC50 : 7.06

3-keto-lithocholic acid

VDRTclin NR

: 6.54

CHEMBL3746404

VDRTclin NR

EC50 : 7.01

CHEMBL3747675

VDRTclin NR

EC50 : 7.02

CHEMBL3746078

VDRTclin NR

EC50 : 7.04

CHEMBL1270254

VDRTclin NR

EC50 : 7.05

CHEMBL239748

VDRTclin NR

IC50 : 7.07

CHEMBL272502

VDRTclin NR

EC50 : 7.81

CHEMBL3747383

VDRTclin NR

EC50 : 7.11

GWAS Traits (6)

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5

1 – 5 of 6

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
testosterone measurement	EFO_0004908	1	1	1		61.7
inflammatory biomarker measurement	EFO_0004872	1	1	0	47.6	50.9
gut microbiome measurement	EFO_0007874	1	1	1		28.4
Diuretic use measurement	EFO_0009928	1	1	1		13.9
eosinophil percentage of leukocytes	EFO_0007991	1	1	1		13.2

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 6

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
testosterone measurement	EFO_0004908	1		61.7
inflammatory biomarker measurement	EFO_0004872	0	47.6	50.9
gut microbiome measurement	EFO_0007874	1		28.4
Diuretic use measurement	EFO_0009928	1		13.9
eosinophil percentage of leukocytes	EFO_0007991	1		13.2

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Orthologs (10)

1 – 5 of 10

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Macaque	vitamin D receptor		706964
Mouse	vitamin D (1,25-dihydroxyvitamin D3) receptor	MGI:103076	22337
Rat	vitamin D receptor	RGD:3959	24873
Dog	vitamin D receptor	VGNC:48249	486588
Horse	vitamin D receptor	VGNC:24898	100034072

Species	Name	OMA	EggNOG	Inparanoid
Macaque	vitamin D receptor
Mouse	vitamin D (1,25-dihydroxyvitamin D3) receptor
Rat	vitamin D receptor
Dog	vitamin D receptor
Horse	vitamin D receptor

Protein Data Bank (49)

1 – 5 of 49

PDB Structure Id	Ligand	Method	Resolution (Å)	M.W. (kDa)	Pub Year	Title

PDB Structure Id	M.W.	Resolution	Pub Year

Pathways (124)

Reactome (13)

KEGG (4)

PathwayCommons (8)

WikiPathways (99)

Gene expression (Transcription) (R-HSA-74160)

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5

1 – 5 of 13

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Gene expression (Transcription)	1452 targets	R-HSA-74160
Reactome	Generic Transcription Pathway	1195 targets	R-HSA-212436
Reactome	Metabolism	2112 targets	R-HSA-1430728
Reactome	Metabolism of lipids	740 targets	R-HSA-556833
Reactome	Metabolism of proteins	2050 targets	R-HSA-392499

Name	Explore in Pharos	Explore in Source
Gene expression (Transcription)	1452 targets	R-HSA-74160
Generic Transcription Pathway	1195 targets	R-HSA-212436
Metabolism	2112 targets	R-HSA-1430728
Metabolism of lipids	740 targets	R-HSA-556833
Metabolism of proteins	2050 targets	R-HSA-392499

Gene Ontology Terms (46)

Functions (15)

Components (5)

Processes (26)

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Items per page:

10

1 – 10 of 15

GO Term	Evidence	Assigned by
calcitriol binding	Inferred from Direct Assay (IDA)	UniProtKB
calcitriol receptor activity	Inferred from Direct Assay (IDA)	UniProtKB
DNA binding	Inferred from Direct Assay (IDA)	MGI
lithocholic acid binding	Inferred from Direct Assay (IDA)	UniProtKB
lithocholic acid receptor activity	Inferred from Direct Assay (IDA)	UniProtKB
retinoid X receptor binding	Inferred from Direct Assay (IDA)	UniProtKB
nuclear receptor transcription coactivator activity	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
RNA polymerase II regulatory region sequence-specific DNA binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
signaling receptor activity	Inferred from Biological aspect of Ancestor (IBA)	GO_Central
transcription factor binding	Inferred from Biological aspect of Ancestor (IBA)	GO_Central

Protein-Protein Interactions (202)

Explore Interacting Targets

1 – 10 of 202

• See Interactions on String-DB

MED1

Tbio

Family: Enzyme

Novelty: 0.00852082

Score: 0.988

Data Source: STRINGDB

NCOA1

Tchem

Family: Epigenetic

Novelty: 0.00344663

Score: 0.974

Data Source: STRINGDB

EP300

Tchem

Family: Epigenetic

Novelty: 0.00055009

Score: 0.969

Data Source: STRINGDB

SMAD3

Tbio

Family: TF

Novelty: 0.00048058

Score: 0.968

Data Source: STRINGDB

CREBBP

Tchem

Family: Epigenetic

Novelty: 0.00111166

Score: 0.964

Data Source: STRINGDB

BAZ1B

Tbio

Family: Epigenetic

Novelty: 0.02374034

Score: 0.962

Data Source: STRINGDB

RXRA

Tclin

Family: NR

Novelty: 0.00244343

Score: 0.955

Data Source: STRINGDB

SMAD4

Tbio

Family: TF

Novelty: 0.00047069

Score: 0.944

Data Source: STRINGDB

RXRB

Tclin

Family: NR

Novelty: 0.01503977

Score: 0.94

Data Source: STRINGDB

RXRG

Tclin

Family: NR

Novelty: 0.01646377

Score: 0.94

Data Source: STRINGDB

Publication Statistics

PubMed Score  1240.33

PubMed score by year

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PubTator Score  4259.25

PubTator score by year

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Amino Acid Sequence

Residue Counts

Protein Sequence

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UniProt Keyword Find Similar Targets

3D-structure
Alternative splicing
Complete proteome
Cytoplasm
Disease mutation
DNA-binding
Metal-binding
Nucleus
Polymorphism
Receptor

GWAS Trait Find Similar Targets

Calcium channel blocker use measurement
Diuretic use measurement
eosinophil percentage of leukocytes
gut microbiome measurement
inflammatory biomarker measurement
testosterone measurement

MGI Phenotype Find Similar Targets

behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
craniofacial phenotype
digestive/alimentary phenotype
endocrine/exocrine gland phenotype
growth/size/body region phenotype
hearing/vestibular/ear phenotype
hematopoietic system phenotype
homeostasis/metabolism phenotype