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Tbio
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: 755.75   (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: 755.75   (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 Ligand: 0
Tclin

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

Active Drug: 0
Protein Data Bank (9)
1 – 5 of 9
PDB Structure Id
Ligand
Method
Resolution (Å)
M.W. (kDa)
Pub Year
Title
PDB Structure Id
M.W.
Resolution
Pub Year
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
Protein-Protein Interactions (172)
1 – 10 of 172
EPN3
Tbio
Novelty: 0.14281801
p_int: 0.998254141
p_ni: 0.001745859
Score: 0.293
Data Source: BioPlex,STRINGDB
PSAT1
Tbio
Family: Enzyme
Novelty: 0.00489383
Score: 0.999
Data Source: STRINGDB
CDC5L
Tbio
Family: TF
Novelty: 0.00617757
Score: 0.98
Data Source: STRINGDB
PGAM1
Tbio
Family: Enzyme
Novelty: 0.0137131
Score: 0.968
Data Source: STRINGDB
PSPH
Tbio
Family: Enzyme
Novelty: 0.01529803
Score: 0.949
Data Source: STRINGDB
PGAM4
Tbio
Family: Enzyme
Novelty: 0.06305271
Score: 0.931
Data Source: STRINGDB
BPGM
Tbio
Family: Enzyme
Novelty: 0.03453422
Score: 0.925
Data Source: STRINGDB
PGAM2
Tbio
Family: Enzyme
Novelty: 0.02989704
Score: 0.919
Data Source: STRINGDB
SRSF10
Tbio
Novelty: 0.01287697
Score: 0.828
Data Source: STRINGDB
SAP18
Tbio
Family: Enzyme
Novelty: 0.05845743
Score: 0.822
Data Source: STRINGDB
Publication Statistics
PubMed Score  755.75

PubMed score by year
PubTator Score  453.71

PubTator score by year
Amino Acid Sequence
Residue Counts
Sequence
MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKL
1-70
QVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMG
70-140
TELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLL
140-210
PSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVIS
210-280
CPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGSP
280-350
KGTIQVITQGTSLKNAGNCLSPAVIVGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGE
350-420
CLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRDLPLLLFRTQTSDPAMLPTMIGLLAEAGV
420-490
RLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF
490-533
MAFANLRKVLISDSLDPCCRKILQDGGLQVVEKQNLSKEELIAELQDCEGLIVRSATKVTADVINAAEKLQVVGRAGTGVDNVDLEAATRKGILVMNTPNGNSLSAAELTCGMIMCLARQIPQATASMKDGKWERKKFMGTELNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVSASFGVQQLPLEEIWPLCDFITVHTPLLPSTTGLLNDNTFAQCKKGVRVVNCARGGIVDEGALLRALQSGQCAGAALDVFTEEPPRDRALVDHENVISCPHLGASTKEAQSRCGEEIAVQFVDMVKGKSLTGVVNAQALTSAFSPHTKPWIGLAEALGTLMRAWAGSPKGTIQVITQGTSLKNAGNCLSPAVIVGLLKEASKQADVNLVNAKLLVKEAGLNVTTSHSPAAPGEQGFGECLLAVALAGAPYQAVGLVQGTTPVLQGLNGAVFRPEVPLRRDLPLLLFRTQTSDPAMLPTMIGLLAEAGVRLLSYQTSLVSDGETWHVMGISSLLPSLEAWKQHVTEAFQFHF