Serine metabolism (WP4688)

Homo sapiens

This pathway shows disorders related to serine metabolism. Disorders resulting from an enzyme defect are highlighted in pink. This pathway was inspired by Chapter 5 (ed. 4) from the book of Blau (ISBN 3642403360 (978-3642403361)), Fig. 5.2.


Amy Kutmon , Denise Slenter , Kristina Hanspers , Yasmin Omar , Egon Willighagen , Eric Weitz , Friederike Ehrhart , and Finterly Hu


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Homo sapiens


Inherited Metabolic Disorders (IMD) Pathways Lipids and LIPID MAPS Rare Diseases


Disease Ontology

PSPH deficiency PHGDH deficiency PSAT deficiency inherited metabolic disorder

Pathway Ontology

serine metabolic pathway


Label Type Compact URI Comment
D-serine Metabolite chebi:35247
3-Phosphoserine Metabolite chebi:57524
Mg2+ Metabolite chebi:18420
NAD+ Metabolite chebi:15846
(2R)-3-phosphoglycerate Metabolite chebi:58272
Phosphatidylserine Metabolite chebi:18303
PLP Metabolite chebi:18405
Glycine Metabolite chebi:57305
Methylene-THF Metabolite chebi:15636
pyruvate Metabolite chebi:15361
glucose Metabolite chebi:17234
H+ Metabolite chebi:15378
D-Glyceraldehyde 3-phosphate Metabolite chebi:29052
3-Phosphohydroxypyruvate Metabolite chebi:18110
L-serine Metabolite chebi:33384
NADH Metabolite chebi:57945
glutamate Metabolite chebi:29985
2-Ketoglutarate Metabolite chebi:16810
H2O Metabolite chebi:15377
Pi Metabolite chebi:43474
dTMP Metabolite chebi:63528
dUMP Metabolite chebi:246422
DHF Metabolite chebi:57451 aka 7,8-dihydrofolate
THF Metabolite chebi:57453
sphingolipids Metabolite chebi:26739
ceramides Metabolite chebi:17761
PHGDH Protein uniprot:O43175
TYMS Protein uniprot:P04818
SHMT1 Protein uniprot:P34896 serine hydroxymethyltransferase 1, cytosolic
SR Protein uniprot:Q9GZT4 Serine racemase
PSAT1 Protein uniprot:Q9Y617
SHMT2 Protein uniprot:P34897 serine hydroxymethyltransferase 2; mitochondrial
DHFR Protein uniprot:P00374
PSPH Protein uniprot:P78330


  1. Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases [Internet]. Blau N, Duran M, Gibson KM, Dionisi-Vici C. Springer; 2014. 0 p. Available from: OpenLibrary Worldcat
  2. Serine racemase modulates intracellular D-serine levels through an alpha,beta-elimination activity. Foltyn VN, Bendikov I, De Miranda J, Panizzutti R, Dumin E, Shleper M, et al. J Biol Chem. 2005 Jan 21;280(3):1754–63. PubMed Europe PMC Scholia
  3. Human phosphoglycerate dehydrogenase produces the oncometabolite D-2-hydroxyglutarate. Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, et al. ACS Chem Biol. 2015 Feb 20;10(2):510–6. PubMed Europe PMC Scholia