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Tchem
PHGDH
D-3-phosphoglycerate dehydrogenase

Protein Summary
Description
Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate. This gene encodes the enzyme which is involved in the early steps of L-serine synthesis in animal cells. L-serine is required for D-serine and other amino acid synthesis. The enzyme requires NAD/NADH as a cofactor and forms homotetramers for activity. Mutations in this gene have been found in a family with congenital microcephaly, psychomotor retardation and other symptoms. Multiple alternatively spliced transcript variants have been found, however the full-length nature of most are not known. [provided by RefSeq, Aug 2011]
Uniprot Accession IDs
Gene Name
Ensembl ID
  • ENST00000641023
  • ENSP00000493175
  • ENSG00000092621
  • ENST00000641597
  • ENSP00000493382

Symbol
  • PGDH3
  • NLS
  • PDG
  • PGD
  • NLS1
  • PGAD
  • PGDH
  • SERA
  • 3PGDH
  • 3-PGDH
  • PHGDHD
  • HEL-S-113
Illumination Graph
Knowledge Table
Most Knowledge About
Knowledge Value (0 to 1 scale)
interacting protein
1
protein complex
1
transcription factor perturbation
0.96
disease perturbation
0.93
kinase perturbation
0.93


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: 1993.72   (req: < 5)
Gene RIFs: 27   (req: <= 3)
Antibodies: 405   (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: 1993.72   (req: >= 5)
Gene RIFs: 27   (req: > 3)
Antibodies: 405   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 17
Tchem

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

Active Ligands: 198
Tclin

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

Active Drug: 0
Protein Sequence and Structure
Residue Counts
Protein Sequence
ProtVista Viewer
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
Thumbnail image for 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.
GlyGen
Thumbnail image for GlyGen
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.
ARCHS4
Thumbnail image for ARCHS4
ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.
Active Ligands (198)
1 – 10 of 198
CHEMBL4541133
Rendered image for CHEMBL4541133
CHEMBL4536737
Rendered image for CHEMBL4536737
CHEMBL4584313
Rendered image for CHEMBL4584313
CHEMBL4436264
Rendered image for CHEMBL4436264
CHEMBL4518579
Rendered image for CHEMBL4518579
CHEMBL4467246
Rendered image for CHEMBL4467246
CHEMBL4520837
Rendered image for CHEMBL4520837
CHEMBL4515492
Rendered image for CHEMBL4515492
CHEMBL4527607
Rendered image for CHEMBL4527607
CHEMBL4579388
Rendered image for CHEMBL4579388
Protein-Protein Interactions (172)
1 – 10 of 172
EPN3
Tbio
Novelty:  0.12685855
p_int:  0.998254141
p_ni:  0.001745859
Score:  0.293
Data Source:  BioPlex,STRINGDB
PSAT1
Tbio
Family:  Enzyme
Novelty:  0.00371113
Score:  0.999
Data Source:  STRINGDB
CDC5L
Tbio
Family:  TF
Novelty:  0.00663599
Score:  0.98
Data Source:  STRINGDB
PGAM1
Tchem
Family:  Enzyme
Novelty:  0.0111272
Score:  0.968
Data Source:  STRINGDB
PSPH
Tbio
Family:  Enzyme
Novelty:  0.01078634
Score:  0.949
Data Source:  STRINGDB
PGAM4
Tbio
Family:  Enzyme
Novelty:  0.03784125
Score:  0.931
Data Source:  STRINGDB
BPGM
Tbio
Family:  Enzyme
Novelty:  0.03437401
Score:  0.925
Data Source:  STRINGDB
PGAM2
Tbio
Family:  Enzyme
Novelty:  0.02438933
Score:  0.919
Data Source:  STRINGDB
SRSF10
Tbio
Novelty:  0.01273022
Score:  0.828
Data Source:  STRINGDB
SAP18
Tbio
Family:  Enzyme
Novelty:  0.03918373
Score:  0.822
Data Source:  STRINGDB
Pathways (15)
Metabolism (R-HSA-1430728)

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
Metabolism
Reactome
Metabolism of amino acids and derivatives
Reactome
Serine biosynthesis
Name
Explore in Pharos
Explore in Source
Metabolism
Metabolism of amino acids and derivatives
Serine biosynthesis
GWAS Traits (19)
GWAS Trait
EFO ID
Study Count
SNP Count
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
blood metabolite measurement
2
2
2
89.1
2
2
0
1.1
81
red blood cell density measurement
1
1
1
79.5
hematocrit
2
2
2
78.7
amino acid measurement
1
1
1
73.7
GWAS Trait
EFO ID
Beta Count
Odds Ratio
Evidence (Mean Rank Score)
Provenance
blood metabolite measurement
2
89.1
0
1.1
81
red blood cell density measurement
1
79.5
hematocrit
2
78.7
amino acid measurement
1
73.7
Find similar targets by:
Orthologs (14)
1 – 5 of 14
Species
Name
Source ID
Gene ID
OMA
EggNOG
Inparanoid
Chimp
phosphoglycerate dehydrogenase
VGNC:1454
739534
Macaque
phosphoglycerate dehydrogenase
713480
Mouse
MGI:1355330
236539
Rat
RGD:61987
58835
Horse
phosphoglycerate dehydrogenase
VGNC:21388
100059940
Species
Name
OMA
EggNOG
Inparanoid
Chimp
phosphoglycerate dehydrogenase
Macaque
phosphoglycerate dehydrogenase
Mouse
Rat
Horse
phosphoglycerate dehydrogenase
Publication Statistics
PubMed Score 1993.72
PubMed score by year
PubTator Score 453.71
PubTator score by year