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.
last edited


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

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Homo sapiens


Inborn Errors of Metabolism (IEM) 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 Identifier 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. Blau N, Duran M, Gibson KM, Dionisi-Vici C. Physician’s Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases [Internet]. Springer; 2014. 867 p. Available from: OpenLibrary Worldcat
  2. Foltyn VN, Bendikov I, De Miranda J, Panizzutti R, Dumin E, Shleper M, et al. Serine racemase modulates intracellular D-serine levels through an alpha,beta-elimination activity. J Biol Chem. 2005 Jan 21;280(3):1754–63. PubMed Europe PMC Scholia
  3. Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, et al. Human phosphoglycerate dehydrogenase produces the oncometabolite D-2-hydroxyglutarate. ACS Chem Biol. 2015 Feb 20;10(2):510–6. PubMed Europe PMC Scholia