Pyrimidine metabolism and related diseases (Homo sapiens)

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1Urea cycleOROTIC ACIDURIATYPE 1HyperammonaemiaCAD-complexMitochondrionSubunit ofOTCdTMPcytidineuridinedUDPTScitrullinethymidineCPS1CTPdUMPOPRTOMP2-DeoxyuridineuridineACT(S)-beta-aminoisobutyrateHCO3-DihydrouracilorotidineUMPRRMTBTPAspartateN-Carbamyl-beta-aminoisobutyric acidDHOUPbeta-AlanineCarbamoylaspartateUTPCarbamoyl-phosphatedihydroorotateRRglutamineCPS2CMPthymineOrnithineCDPDHODHOrotatedihydrothyminePRPPN-Carbamoyl-beta-alanineUMPH1uracilDPDOMPDCUDPOrotatedihydroorotateCarbamoyl-phosphateglutamineDHPHCO3-CPS2DHOACTOPRTOMPDCUMPS-complex+ PRPPOROTIC ACIDURIATYPE 2HYPER-BETA-ALANINEMIAMitochondrialribonucleotide reductasesubunit 2deciciencyType 8AType 8BThymidine phosphorylase deficiencyDihydropyrimidine dehydrogenase deficiencyDihydropyrimidinuriaBeta-ureidopropionase deficiencyPyrimidine 5'-nucleotidasesuperactivityUMPH2UMPHUMPH1UMPH2UMPHPyrimidine 5'-nucleotidasesuperactivityUMPH1 deficiencyUMPH1 deficiencyBeta-aminoisobutyric aciduria; baiba


Overview of pyrimidine metabolism and related diseases. Disorders resulting from an enzyme defect are highlighted in pink (one disease is depicted in orange, since there appears to be no clinical difference between type 2 and 1 of orotic aciduria, therefore researchers believe that type 2 does not exist officially).

Metabolic markers are highlighted in dark purple. The link to the Urea cycle is depicted for clarity.

This pathway was inspired by Chapter 41 of the book of Blau (ISBN 978-3-642-40337-8).

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Ontology Terms



  1. Blau, N., Duran, M., Gibson, K.M., Donisi-Vici, C.; ''Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases, Chapter 41''; ISBN 978-3-642-40337-8, 2014


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102678view09:28, 17 January 2019DeSlModified description
102677view09:26, 17 January 2019DeSlChanged interactions to graphical lines for diseases.
98925view05:21, 16 October 2018EgonwModified description
98283view11:19, 16 August 2018EgonwReplaced secondary ChEBI IDs with primary IDs.
98262view12:59, 15 August 2018DeSlModified description
98261view12:57, 15 August 2018DeSlAdded IDs
98260view11:58, 15 August 2018DeSlAdded more IDs.
98259view11:49, 15 August 2018DeSlAdded IDs for added metabolites
98258view11:43, 15 August 2018DeSlConnected some more steps between CTP and cytidine; connected last diseases (several IDs where just for the gene, not the disease).
98257view10:55, 15 August 2018DeSlChanged diseases to textlabels, changed layout slightly.
98256view09:51, 15 August 2018DeSlModified description
98202view09:41, 7 August 2018MkutmonModified title
96741view06:02, 2 April 2018EgonwReplaced secondary ChEBI identifiers with primary identifiers.
96674view08:21, 26 March 2018DeSlAdded more disease nodes (still have to connect them to related proteins).
96668view13:37, 25 March 2018DeSlAdded complex linked to diseases
96667view13:21, 25 March 2018DeSlAdded more side metabolites, changed color of marker metabolites to purple
96666view13:09, 25 March 2018DeSlModified description
96546view21:18, 17 March 2018DeSlOntology Term : 'beta-ureidopropionase deficiency pathway' added !
96545view21:17, 17 March 2018DeSlOntology Term : 'dihydropyrimidine dehydrogenase deficiency pathway' added !
96544view21:17, 17 March 2018DeSlOntology Term : 'dihydropyrimidine dehydrogenase deficiency' added !
96543view21:17, 17 March 2018DeSlOntology Term : 'oroticaciduria 1 disease pathway' added !
96542view21:16, 17 March 2018DeSlOntology Term : 'orotic aciduria' added !
96541view21:14, 17 March 2018DeSlOntology Term : 'pyrimidine metabolic disorder' added !
96540view21:14, 17 March 2018DeSlOntology Term : 'pyrimidine metabolic pathway' added !
96539view21:13, 17 March 2018DeSlOntology Term : 'inborn error purine-pyrimidine metabolism disease pathway' added !
96536view21:11, 17 March 2018DeSlAdded lit. ref.
96531view20:58, 17 March 2018DeSlChanged KEGG genes datasource to Enzyme Nomenclature, removed EC for ID number.
96530view20:56, 17 March 2018DeSlAdded OMIM IDs for diseases
96268view22:21, 2 March 2018RoelModified description
96267view22:20, 2 March 2018RoelRemoved redundant node
96266view22:18, 2 March 2018RoelNew pathway

External references


View all...
NameTypeDatabase referenceComment
(S)-beta-aminoisobutyrateMetaboliteCHEBI:18188 (ChEBI)
+ PRPPMetaboliteCHEBI:17111 (ChEBI)
2-DeoxyuridineMetaboliteCHEBI:16450 (ChEBI)
ACTGeneProduct2.1.3.2 (KEGG Genes)
AspartateMetaboliteCHEBI:132943 (ChEBI)
CDPMetaboliteCHEBI:58069 (ChEBI) CDP 3-, charge needed for conversion can take place
CMPMetaboliteQ27104867 (Wikidata) CMP (2-), charge needed for conversion can take place
CPS1GeneProduct6.3.4.16 (KEGG Genes)
CPS2GeneProduct6.3.5.5 (Enzyme Nomenclature)
CTPMetaboliteCHEBI:17677 (ChEBI)
Carbamoyl-phosphateMetaboliteCHEBI:17672 (ChEBI)
CarbamoylaspartateMetaboliteCHEBI:15859 (ChEBI)
DHODHMetaboliteCHEBI:77103 (ChEBI)
DHPProteinQ14117 (Uniprot-TrEMBL)
DPDProteinQ12882 (Uniprot-TrEMBL)
DihydrouracilMetaboliteCHEBI:15901 (ChEBI)
HCO3-Metabolite17544 (ChEBI)
N-Carbamoyl-beta-alanineMetaboliteCHEBI:18261 (ChEBI)
N-Carbamyl-beta-aminoisobutyric acidMetaboliteCHEBI:1670 (ChEBI)
OMPMetaboliteCHEBI:15842 (ChEBI) Orotidylic acid
OMPDCGeneProduct4.1.1.23 (Enzyme Nomenclature)
OPRTGeneProduct2.4.2.10 (Enzyme Nomenclature)
OTCProteinP00480 (Uniprot-TrEMBL)
OrnithineMetaboliteCHEBI:16176 (ChEBI)
OrotateMetaboliteCHEBI:16742 (ChEBI)
PRPPMetaboliteCHEBI:17111 (ChEBI)
RRGeneProduct1.17.4.1 (Enzyme Nomenclature)
RRMTBProteinQ7LG56 (Uniprot-TrEMBL)
TPProteinE5KRG5 (Uniprot-TrEMBL)
TSProteinP04818 (Uniprot-TrEMBL)
UDPMetaboliteCHEBI:17659 (ChEBI)
UMPMetaboliteCHEBI:16695 (ChEBI)
UMPH1ProteinQ9H0P0 (Uniprot-TrEMBL)
  • aka P5N1
  • Enzymes and reactions added with info from
UMPH2ProteinQ8TCD5 (Uniprot-TrEMBL)
  • aka NT5C
  • Enzymes and reactions added with info from
UMPHProtein3.1.3.5 (Enzyme Nomenclature)
  • aka P5N
  • Enzymes and reactions added with info from
UPProteinF8WC94 (Uniprot-TrEMBL)
UTPMetaboliteCHEBI:46398 (ChEBI)
beta-AlanineMetaboliteCHEBI:16958 (ChEBI)
citrullineMetaboliteCHEBI:18211 (ChEBI)
cytidineMetaboliteCHEBI:17562 (ChEBI)
dTMPMetaboliteCHEBI:63528 (ChEBI)
dUDPMetaboliteCHEBI:28850 (ChEBI)
dUMPMetaboliteCHEBI:17622 (ChEBI)
dihydroorotateMetaboliteQ27114007 (Wikidata)
dihydrothymineMetaboliteQ3027885 (Wikidata)
glutamineMetaboliteCHEBI:28300 (ChEBI)
orotidineMetaboliteCHEBI:25722 (ChEBI)
thymidineMetaboliteCHEBI:17748 (ChEBI)
thymineMetaboliteCHEBI:17821 (ChEBI)
uracilMetaboliteCHEBI:17568 (ChEBI)
uridineMetaboliteCHEBI:16704 (ChEBI)

Annotated Interactions

No annotated interactions

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