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Pyrimidine metabolism

SourceIDPathway
PathWhizPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG00240 Map00240

Pathway Metabolites

YMDB ID Name
CAS Number
IUPAC Name Formula
Weight
Structure
YMDB00002L-Glutamine
56-85-9
(2S)-2-amino-4-carbamoylbutanoic acidC5H10N2O3
146.1445
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YMDB00003Urea
57-13-6
ureaCH4N2O
60.0553
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YMDB00025Orotidylic acid
2149-82-8
3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acidC10H13N2O11P
368.1908
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YMDB00027Ureidosuccinic acid
13184-27-5
(2S)-2-(carbamoylamino)butanedioic acidC5H8N2O5
176.1274
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YMDB00049Uridine 5'-monophosphate
58-97-9
{[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acidC9H13N2O9P
324.1813
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YMDB00051Cytidine
65-46-3
4-amino-1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-oneC9H13N3O5
243.2166
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YMDB00064CDP
63-38-7
[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidC9H15N3O11P2
403.1764
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YMDB00079Dihydrofolic acid
4033-27-6
(2S)-2-[(4-{[(2-amino-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)methyl]amino}phenyl)formamido]pentanedioic acidC19H21N7O6
443.4133
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YMDB00082Carbamoylphosphate
590-55-6
(carbamoyloxy)phosphonic acidCH4NO5P
141.0199
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YMDB00085Flavin Mononucleotide
146-17-8
{[(2R,3S,4S)-5-{7,8-dimethyl-2,4-dioxo-2H,3H,4H,10H-benzo[g]pteridin-10-yl}-2,3,4-trihydroxypentyl]oxy}phosphonic acidC17H21N4O9P
456.3438
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YMDB00088Ubiquinone Q1
727-81-1
2,3-dimethoxy-5-methyl-6-(3-methylbut-2-en-1-yl)cyclohexa-2,5-diene-1,4-dioneC14H18O4
250.2903
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YMDB00098Uracil
66-22-8
1,2,3,4-tetrahydropyrimidine-2,4-dioneC4H4N2O2
112.0868
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YMDB00109Adenosine triphosphate
56-65-5
({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC10H16N5O13P3
507.181
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YMDB00127Uridine
58-96-8
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneC9H12N2O6
244.2014
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YMDB001625-Thymidylic acid
365-07-1
{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy}phosphonic acidC10H15N2O8P
322.2085
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YMDB00194Iron(3+)
20074-52-6
iron(3+) ionFe
55.845
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YMDB00195Beta-Alanine
107-95-9
3-aminopropanoic acidC3H7NO2
89.0932
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YMDB00201Deoxyuridine triphosphate
1173-82-6
({[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC9H15N2O14P3
468.1417
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YMDB00205dTDP
491-97-4
{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}phosphonic acidC10H16N2O11P2
402.1884
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YMDB00206dCMP
1032-65-1
{[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acidC9H14N3O7P
307.1971
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YMDB00212Uridine diphosphate glucose
133-89-1
[({[(2S,3R,4S,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acidC15H24N2O17P2
566.3018
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YMDB00219Pyrophosphate
14000-31-8
(phosphonooxy)phosphonic acidH4O7P2
177.9751
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YMDB00221dUMP
964-26-1
{[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}phosphonic acidC9H13N2O8P
308.1819
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YMDB00271L-Glutamic acid
56-86-0
(2S)-2-aminopentanedioic acidC5H9NO4
147.1293
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YMDB00279Cytidine triphosphate
65-47-4
({[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC9H16N3O14P3
483.1563
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YMDB00307Uridine 5'-diphosphate
58-98-0
[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidC9H14N2O12P2
404.1612
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YMDB00326Uridine triphosphate
63-39-8
({[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC9H15N2O15P3
484.1411
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YMDB00379Iron(2+)
15438-31-0
λ²-iron(2+) ionFe
55.845
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YMDB00396L-Dihydroorotic acid
5988-19-2
(4S)-2,6-dioxo-1,3-diazinane-4-carboxylic acidC5H6N2O4
158.1121
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YMDB00402Phosphoribosyl pyrophosphate
7540-64-9
[({[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acidC5H13O14P3
390.0696
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YMDB00405Orotic acid
65-86-1
2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acidC5H4N2O4
156.0963
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YMDB00406Cytidine monophosphate
63-37-6
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acidC9H14N3O8P
323.1965
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YMDB00415UDP-D-glucose
133-89-1
[({[(2R,3S,4R,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphinic acidC15H24N2O17P2
566.3018
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YMDB00423Ammonium
14798-03-9
azaniumH4N
18.0385
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YMDB005042'-Deoxycytidine
951-77-9
4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-oneC9H13N3O4
227.2172
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YMDB005052'-Deoxyguanosine
2564-35-4
2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-oneC10H13N5O4
267.2413
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YMDB00507Thymidine
50-89-5
1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneC10H14N2O5
242.2286
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YMDB005082'-Deoxyuridine
951-78-0
1-[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneC9H12N2O5
228.202
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YMDB00558GTP
86-01-1
({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC10H16N5O14P3
523.1804
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YMDB00651Cytosine
71-30-7
6-amino-1,2-dihydropyrimidin-2-oneC4H5N3O
111.102
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YMDB00658dCTP
2056-98-6
({[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC9H16N3O13P3
467.1569
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YMDB006612-deoxy-D-ribose
533-67-5
(3S,4R)-3,4,5-trihydroxypentanalC5H10O4
134.1305
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YMDB006632-deoxy-D-ribofuranose 1-phosphate
17210-42-3
{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acidC5H11O7P
214.1104
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YMDB00744dGTP
2564-35-4
({[({[(2R,3S,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)phosphonic acidC10H16N5O13P3
507.181
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YMDB00745dTTP
365-08-2
{[hydroxy({[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy})phosphoryl]oxy}phosphonic acidC10H17N2O14P3
482.1683
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YMDB00746dUDP
4208-67-7
[({[(2R,3S,5R)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidC9H14N2O11P2
388.1618
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YMDB00780Pseudouridine 5'-phosphate
1157-60-4
{[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acidC9H13N2O9P
324.1813
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YMDB00782potassium atompotassiumK
39.0983
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YMDB00862hydron
12408-02-5
hydronH
1.00794
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YMDB00885Thymine
65-71-4
5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneC5H6N2O2
126.1133
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YMDB00890water
7732-18-5
waterH2O
18.0153
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YMDB00896L-Aspartic acid
56-84-8
(2S)-2-aminobutanedioic acidC4H7NO4
133.1027
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YMDB00907phosphate
14265-44-2
phosphoric acidO4P
94.9714
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YMDB00912Carbon dioxide
124-38-9
methanedioneCO2
44.0095
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YMDB00914ADP
58-64-0
[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidC10H15N5O10P2
427.2011
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YMDB00916dCDP
800-73-7
[({[(2R,3S,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acidC9H15N3O10P2
387.177
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YMDB01008N-Carbamoyl-L-aspartate
13184-27-5
(2S)-2-(carbamoylamino)butanedioateC5H6N2O5
174.1115
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YMDB01016(S)-Dihydroorotate
5988-19-2
C5H5N2O4
157.1042
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YMDB01520Magnesium
7439-95-4
magnesium(2+) ionMg
24.305
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YMDB01527Zinc
7440-66-6
zinc(2+) ionZn
65.409
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YMDB161154,5-Dihydroorotic acid2,6-dioxo-1,3-diazinane-4-carboxylic acidC5H6N2O4
158.1121
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YMDB16117Potassiumpotassium(1+) ionK
39.0983
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YMDB16118Hydrogen carbonatecarbonic acidCHO3
61.0168
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YMDB16248QH(2)2,3-dimethoxy-5-methyl-6-(3-methylbut-2-en-1-yl)benzene-1,4-diolC14H20O4
252.3062
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YMDB162524Fe-4Stetrakis(lambda1-iron(1+) ion) tetrasulfane tetrasulfanideFe4H12S8
491.96
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YMDB162795,10-methenyltetrahydrofolate mono-L-glutamate(6aR)-3-amino-8-(4-{[(1S)-1,3-dicarboxypropyl]carbamoyl}phenyl)-1-oxo-1H,2H,5H,6H,6aH,7H,8H-10lambda5-imidazo[1,5-f]pteridin-10-yliumC20H20N7O6
454.424
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Pathway Proteins

Uniprot ID Gene Name
Locus
Name Type Metabolites
P07258CPA1
YOR303W
Carbamoyl-phosphate synthase arginine-specific small chainEnzyme
P07259URA2
YJL130C
Protein URA1Enzyme
P03965CPA2
YJR109C
Carbamoyl-phosphate synthase arginine-specific large chainEnzyme
P28274URA7
YBL039C
CTP synthase 1Enzyme
P38627URA8
YJR103W
CTP synthase 2Enzyme
P13298URA5
YML106W
Orotate phosphoribosyltransferase 1Enzyme
P30402URA10
YMR271C
Orotate phosphoribosyltransferase 2Enzyme
P03962URA3
YEL021W
Orotidine 5'-phosphate decarboxylaseEnzyme
P20051URA4
YLR420W
DihydroorotaseEnzyme
Q05788PNP1
YLR209C
Purine nucleoside phosphorylaseEnzyme
Q12084
YDR020C
Putative uridine kinase YDR020CEnzyme
P40009YND1
YER005W
Golgi apyraseEnzyme
P27515URK1
YNR012W
Uridine kinaseEnzyme
Q06549CDD1
YLR245C
Cytidine deaminaseEnzyme
P09938RNR2
YJL026W
Ribonucleoside-diphosphate reductase small chain 1Enzyme
P36010YNK1
YKL067W
Nucleoside diphosphate kinaseEnzyme
P21524RNR1
YER070W
Ribonucleoside-diphosphate reductase large chain 1Enzyme
P06785TMP1
YOR074C
Thymidylate synthaseEnzyme
Q12178FCY1
YPR062W
Cytosine deaminaseEnzyme
P06773DCD1
YHR144C
Deoxycytidylate deaminaseEnzyme
P00572CDC8
YJR057W
Thymidylate kinaseEnzyme
Q12273TY1B-OL
YOL103W-B
Transposon Ty1-OL Gag-Pol polyproteinTransporter
P33317DUT1
YBR252W
Deoxyuridine 5'-triphosphate nucleotidohydrolaseEnzyme
Q12113TY2B-OR1
YOR192C-B
Transposon Ty2-OR1 Gag-Pol polyproteinEnzyme
P49723RNR4
YGR180C
Ribonucleoside-diphosphate reductase small chain 2Enzyme
P28272URA1
YKL216W
Dihydroorotate dehydrogenaseEnzyme
P29509TRR1
YDR353W
Thioredoxin reductase 1Enzyme
P38816TRR2
YHR106W
Thioredoxin reductase 2, mitochondrialEnzyme
P18562FUR1
YHR128W
Uracil phosphoribosyltransferaseEnzyme
Q04179URH1
YDR400W
Uridine nucleosidaseEnzyme
P21672RNR3
Ribonucleoside-diphosphate reductase large chain 2Enzyme