Tchem APOB Apolipoprotein B-100

Protein Summary

Description

Apolipoprotein B is a major protein constituent of chylomicrons (apo B-48), LDL (apo B-100) and VLDL (apo B-100). Apo B-100 functions as a recognition signal for the cellular binding and internalization of LDL particles by the apoB/E receptor. This gene product is the main apolipoprotein of chylomicrons and low density lipoproteins. It occurs in plasma as two main isoforms, apoB-48 and apoB-100: the former is synthesized exclusively in the gut and the latter in the liver. The intestinal and the hepatic forms of apoB are encoded by a single gene from a single, very long mRNA. The two isoforms share a common N-terminal sequence. The shorter apoB-48 protein is produced after RNA editing of the apoB-100 transcript at residue 2180 (CAA->UAA), resulting in the creation of a stop codon, and early translation termination. Mutations in this gene or its regulatory region cause hypobetalipoproteinemia, normotriglyceridemic hypobetalipoproteinemia, and hypercholesterolemia due to ligand-defective apoB, diseases affecting plasma cholesterol and apoB levels. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• P04114
• O00502
• P78479
• P78480
• P78481
• Q13779
• Q13785
• Q13786
• Q13787
• Q13788
• Q4ZG63
• Q53QC8
• Q7Z600
• Q9UMN0
• Apo B-100

Gene Name

• APOB

Ensembl ID

• ENST00000233242
• ENSP00000233242
• ENSG00000084674

Symbol

• FLDB
• LDLCQ4
• apoB-48
• apoB-100

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological term	1
metabolite	1
protein domain	1
biological process	0.98
trait	0.97

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: 12323.95   (req: < 5)

Gene RIFs: 506   (req: <= 3)

Antibodies: 1048   (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: 12323.95   (req: >= 5)

Gene RIFs: 506   (req: > 3)

Antibodies: 1048   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 47

Tchem

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

Active Ligands: 49

Tclin

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

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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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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Active Ligands (49)

Explore Active Ligands

1 – 10 of 49

CHEMBL423915

APOBTchem

pIC50 : 8.19

CHEMBL142450

APOBTchem

pIC50 : 9.15

CHEMBL143626

APOBTchem

pIC50 : 8.72

CHEMBL341974

APOBTchem

pIC50 : 8.62

CHEMBL142975

APOBTchem

pIC50 : 8.8

CHEMBL139834

APOBTchem

pIC50 : 9

CHEMBL142332

APOBTchem

pIC50 : 8.39

CHEMBL359428

APOBTchem

pIC50 : 8.74

CHEMBL142733

APOBTchem

pIC50 : 8.66

CHEMBL422295

APOBTchem

pIC50 : 8.74

Protein-Protein Interactions (578)

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1 – 10 of 578

• See Interactions on String-DB

RPN2

Tbio

Family:  Enzyme

Novelty:  0.01796569

p_int:  0.984217839

p_ni:  0.015782161

Data Source:  BioPlex

YIPF3

Tbio

Novelty:  0.12021667

p_int:  0.983956843

p_ni:  0.016043005

p_wrong:  1.52e-7

Data Source:  BioPlex

LITAF

Tbio

Family:  TF

Novelty:  0.0097203

p_int:  0.978465593

p_ni:  0.021534407

Data Source:  BioPlex

TMEM128

Tdark

Novelty:  5.15874803

p_int:  0.969848017

p_ni:  0.030151983

Data Source:  BioPlex

ZFYVE27

Tbio

Novelty:  0.0563358

p_int:  0.959199115

p_ni:  0.040800882

p_wrong:  2e-9

Data Source:  BioPlex

ZDHHC11

Tdark

Family:  Enzyme

Novelty:  0.35249931

p_int:  0.956770367

p_ni:  0.043229632

Score:  0.177

Data Source:  BioPlex,STRINGDB

SLC37A3

Tdark

Family:  Transporter

Novelty:  0.21571546

p_int:  0.934312432

p_ni:  0.065684641

p_wrong:  0.000002926

Data Source:  BioPlex

AUP1

Tbio

Novelty:  0.0418459

p_int:  0.878641691

p_ni:  0.121358305

p_wrong:  4e-9

Score:  0.545

Data Source:  BioPlex,STRINGDB

SSR3

Tbio

Novelty:  0.05838475

p_int:  0.876032728

p_ni:  0.123095459

p_wrong:  0.000871813

Data Source:  BioPlex

RTP2

Tbio

Novelty:  0.05972678

p_int:  0.875653065

p_ni:  0.123511313

p_wrong:  0.000835622

Data Source:  BioPlex

Pathways (53)

Reactome (42)

KEGG (3)

PathwayCommons (2)

WikiPathways (6)

Binding and Uptake of Ligands by Scavenger Receptors (R-HSA-2173782)

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Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Binding and Uptake of Ligands by Scavenger Receptors	116 targets	R-HSA-2173782
Reactome	Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Reactome	Cell surface interactions at the vascular wall	211 targets	R-HSA-202733
Reactome	Chylomicron assembly	10 targets	R-HSA-8963888
Reactome	Chylomicron clearance	5 targets	R-HSA-8964026

Name	Explore in Pharos	Explore in Source
Binding and Uptake of Ligands by Scavenger Receptors	116 targets	R-HSA-2173782
Cargo recognition for clathrin-mediated endocytosis	105 targets	R-HSA-8856825
Cell surface interactions at the vascular wall	211 targets	R-HSA-202733
Chylomicron assembly	10 targets	R-HSA-8963888
Chylomicron clearance	5 targets	R-HSA-8964026

Gene Ontology Terms (72)

Functions (5)

Components (25)

Processes (42)

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10

1 – 5 of 5

GO Term	Evidence	Assigned by
heparin binding	Inferred from Direct Assay (IDA)	BHF-UCL
phospholipid binding	Inferred from Direct Assay (IDA)	BHF-UCL
lipase binding	Inferred from Physical Interaction (IPI)	BHF-UCL
cholesterol transporter activity	Inferred from Mutant Phenotype (IMP)	BHF-UCL
low-density lipoprotein particle receptor binding	Inferred from Mutant Phenotype (IMP)	BHF-UCL

GWAS Traits (37)

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 37

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	25	41	81	4.1	99.9
apolipoprotein B measurement	EFO_0004615	2	21	21		99.9
total cholesterol measurement	EFO_0004574	14	37	67	3.6	99.9
triglyceride measurement	EFO_0004530	16	22	46	6	99.8
high density lipoprotein cholesterol measurement	EFO_0004612	10	14	31		99.6

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

1 – 5 of 37

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
low density lipoprotein cholesterol measurement	EFO_0004611	81	4.1	99.9
apolipoprotein B measurement	EFO_0004615	21		99.9
total cholesterol measurement	EFO_0004574	67	3.6	99.9
triglyceride measurement	EFO_0004530	46	6	99.8
high density lipoprotein cholesterol measurement	EFO_0004612	31		99.6

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Find similar targets by:

UniProt Keyword Find Similar Targets

No Header	No Header
Acetylation
Atherosclerosis
Cholesterol metabolism
Chylomicron
Complete proteome
Cytoplasm
Direct protein sequencing
Disease mutation
Disulfide bond
Glycoprotein

GWAS Trait Find Similar Targets

No Header	No Header
alkaline phosphatase measurement
apolipoprotein A 1 measurement
apolipoprotein B measurement
aspartate aminotransferase measurement
atrial fibrillation
blood metabolite measurement
butyrylcholinesterase measurement
C-reactive protein measurement
coronary artery disease
ferritin measurement

MGI Phenotype Find Similar Targets

No Header	No Header
cardiovascular system phenotype
cellular phenotype
embryo phenotype
growth/size/body region phenotype
homeostasis/metabolism phenotype
liver/biliary system phenotype
mortality/aging
nervous system phenotype
reproductive system phenotype

Orthologs (10)

1 – 5 of 10

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	apolipoprotein B	VGNC:171	459058
Macaque	apolipoprotein B		702937
Mouse	apolipoprotein B	MGI:88052	238055
Rat	apolipoprotein B	RGD:2129	54225
Dog	apolipoprotein B	VGNC:37994	475680

Species	Name	OMA	EggNOG	Inparanoid
Chimp	apolipoprotein B
Macaque	apolipoprotein B
Mouse	apolipoprotein B
Rat	apolipoprotein B
Dog	apolipoprotein B

Publication Statistics

PubMed Score 12323.95

PubMed score by year

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PubTator Score 8443.98

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