TCA Cycle

Source	ID	Pathway
PathWhiz	PW002377

Pathway Metabolites

YMDB ID	Name CAS Number	IUPAC Name	Formula Weight
YMDB00026	Isocitric acid 320-77-4	1-hydroxypropane-1,2,3-tricarboxylic acid	C₆H₈O₇ 192.1235
YMDB00045	Coenzyme A 85-61-0	{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({hydroxy[(3R)-3-hydroxy-2,2-dimethyl-3-({2-[(2-sulfanylethyl)carbamoyl]ethyl}carbamoyl)propoxy]phosphoryl}oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid	C₂₁H₃₆N₇O₁₆P₃S 767.534
YMDB00086	Citric acid 77-92-9	2-hydroxypropane-1,2,3-tricarboxylic acid	C₆H₈O₇ 192.1235
YMDB00101	Fumaric acid 110-17-8	(2E)-but-2-enedioic acid	C₄H₄O₄ 116.0722
YMDB00109	Adenosine 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 acid	C₁₀H₁₆N₅O₁₃P₃ 507.181
YMDB00110	NAD 53-84-9	1-[(2R,3R,4S,5R)-5-[({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1lambda5-pyridin-1-ylium	C₂₁H₂₈N₇O₁₄P₂ 664.433
YMDB00143	NADH 58-68-4	[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(2R,3S,4R,5R)-5-(3-carbamoyl-1,4-dihydropyridin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy})phosphinic acid	C₂₁H₂₉N₇O₁₄P₂ 665.441
YMDB00153	Oxoglutaric acid 328-50-7	2-oxopentanedioic acid	C₅H₆O₅ 146.0981
YMDB00175	Pyruvic acid 127-17-3	2-oxopropanoic acid	C₃H₄O₃ 88.0621
YMDB00235	Oxalacetic acid 328-42-7	2-oxobutanedioic acid	C₄H₄O₅ 132.0716
YMDB00257	Guanosine diphosphate 146-91-8	[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-3H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid	C₁₀H₁₅N₅O₁₁P₂ 443.2005
YMDB00280	(S)-Malic acid 97-67-6	(2S)-2-hydroxybutanedioic acid	C₄H₆O₅ 134.0874
YMDB00282	Biotin 58-85-5	5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid	C₁₀H₁₆N₂O₃S 244.311
YMDB00296	FAD 146-14-5	{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(2R,3S,4S)-5-{7,8-dimethyl-2,4-dioxo-2H,3H,4H,10H-benzo[g]pteridin-10-yl}-2,3,4-trihydroxypentyl]oxy}(hydroxy)phosphoryl)oxy]phosphinic acid	C₂₇H₃₃N₉O₁₅P₂ 785.5497
YMDB00312	Acetyl-CoA 72-89-9	{[(2R,3S,4R,5R)-2-({[({[(3R)-3-[(2-{[2-(acetylsulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-3-hydroxy-2,2-dimethylpropoxy](hydroxy)phosphoryl}oxy)(hydroxy)phosphoryl]oxy}methyl)-5-(6-amino-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}phosphonic acid	C₂₃H₃₈N₇O₁₇P₃S 809.571
YMDB00338	Succinic acid 110-15-6	butanedioic acid	C₄H₆O₄ 118.088
YMDB00381	Thiamine pyrophosphate 154-87-0	3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium	C₁₂H₁₉N₄O₇P₂S 425.314
YMDB00514	Succinyl-CoA 604-98-8	4-[(2-{3-[(2R)-3-[({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-4-oxobutanoic acid	C₂₅H₄₀N₇O₁₉P₃S 867.607
YMDB00558	GTP 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 acid	C₁₀H₁₆N₅O₁₄P₃ 523.1804
YMDB00597	FADH2 1910-41-4	{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(2R,3S,4S)-5-{7,8-dimethyl-2,4-dioxo-1H,2H,3H,4H,5H,10H-benzo[g]pteridin-10-yl}-2,3,4-trihydroxypentyl]oxy}(hydroxy)phosphoryl)oxy]phosphinic acid	C₂₇H₃₅N₉O₁₅P₂ 787.5656
YMDB00630	cis-aconitic acid 585-84-2	(1Z)-prop-1-ene-1,2,3-tricarboxylic acid	C₆H₆O₆ 174.1082
YMDB00697	lipoamide 940-69-2	5-(1,2-dithiolan-3-yl)pentanamide	C₈H₁₅NOS₂ 205.341
YMDB00862	hydron 12408-02-5	hydron	H 1.00794
YMDB00890	water 7732-18-5	water	H₂O 18.0153
YMDB00902	ubiquinol 56275-39-9	2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]benzene-1,4-diol	C₄₉H₇₈O₄ 731.1412
YMDB00907	phosphate 14265-44-2	phosphoric acid	O₄P 94.9714
YMDB00912	Carbon dioxide 124-38-9	methanedione	CO₂ 44.0095
YMDB00914	ADP 58-64-0	[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid	C₁₀H₁₅N₅O₁₀P₂ 427.2011
YMDB01064	(S)-malate(2-)	(2S)-2-hydroxybutanedioate	C₄H₄O₅ 132.0716
YMDB01093	thiamine(1+) diphosphate(1-)	3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(hydrogen phosphonatooxy)(hydroxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium	C₁₂H₁₈N₄O₇P₂S 424.306
YMDB01520	Magnesium 7439-95-4	magnesium(2+) ion	Mg 24.305
YMDB01521	Manganese 7439-96-5	manganese(2+) ion	Mn 54.938045
YMDB16118	Hydrogen carbonate	carbonic acid	CHO₃ 61.0168
YMDB16129	Coenzyme Q10	2-[(2E,6E,10E,14E,18E,22E,26Z,30E,34E)-3,7,11,15,19,23,27,31,35,39-decamethyltetraconta-2,6,10,14,18,22,26,30,34,38-decaen-1-yl]-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione	C₅₉H₉₀O₄ 863.3435
YMDB16248	QH(2)	2,3-dimethoxy-5-methyl-6-(3-methylbut-2-en-1-yl)benzene-1,4-diol	C₁₄H₂₀O₄ 252.3062
YMDB16252	4Fe-4S	tetrakis(lambda1-iron(1+) ion) tetrasulfane tetrasulfanide	Fe₄H₁₂S₈ 491.96

Pathway Proteins

Uniprot ID	Gene Name Locus	Name	Type	Metabolites
P53598	LSC1 YOR142W	Succinyl-CoA ligase [ADP-forming] subunit alpha, mitochondrial	Enzyme	Coenzyme A Adenosine triphosphate Guanosine diphosphate Succinic acid Succinyl-CoA GTP itaconic acid itaconyl-CoA phosphate ADP
P43635	CIT3 YPR001W	Citrate synthase 3	Enzyme	Coenzyme A Citric acid Oxalacetic acid Acetyl-CoA propionyl-CoA hydron water (2S,3S)-2-Methylcitric acid
P53312	LSC2 YGR244C	Succinyl-CoA ligase [ADP-forming] subunit beta, mitochondrial	Enzyme	Coenzyme A Adenosine triphosphate Guanosine diphosphate Succinic acid Succinyl-CoA GTP itaconic acid itaconyl-CoA phosphate ADP
P12695	PDA2 YNL071W	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial	Enzyme	Coenzyme A NAD NADH Oxoglutaric acid Acetyl-CoA Succinyl-CoA hydron Carbon dioxide
P41921	GLR1 YPL091W	Glutathione reductase	Enzyme	Coenzyme A Oxidized glutathione NAD NADH Oxoglutaric acid Glutathione Pyruvic acid Acetyl-CoA Thiamine pyrophosphate NADPH NADP Succinyl-CoA glutathione disulfide hydron Carbon dioxide 2-(a-Hydroxyethyl)thiamine diphosphate
P32614	YEL047C	Fumarate reductase	Enzyme	Flavin Mononucleotide Fumaric acid NAD NADH FAD Succinic acid NAD(+) FADH2 FMNH2 Coenzyme Q10
P21801	SDH2 YLL041C	Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial	Enzyme	Ubiquinone Q1 Fumaric acid FAD Succinic acid FADH2 Ubiquinone-6 ubiquinol Ubiquinol-6 Coenzyme Q10
P08417	FUM1 YPL262W	Fumarate hydratase, mitochondrial	Enzyme	Ammonia Fumaric acid (S)-Malic acid water L-Aspartic acid
P07264	LEU1 YGL009C	3-isopropylmalate dehydratase	Enzyme	2-Isopropylmalic acid 3-Isopropylmalate 2-Isopropylmaleic acid water
Q00955	FAS3 YNR016C	Acetyl-CoA carboxylase	Enzyme	Adenosine triphosphate Pyruvic acid Pyrophosphate Oxalacetic acid Acetyl-CoA Carbonic acid malonyl-CoA hydron phosphate Carbon dioxide ADP Hydrogen carbonate
P22133	MDH2 YOL126C	Malate dehydrogenase, cytoplasmic	Enzyme	NAD NADH Oxalacetic acid (S)-Malic acid NAD(+) hydron
P40495	LYS12 YIL094C	Homoisocitrate dehydrogenase, mitochondrial	Enzyme	Isocitric acid NAD Oxoadipic acid NADH Homoisocitric acid Oxoglutaric acid NAD(+) 2-Oxaloglutaric acid hydron Carbon dioxide (1R,2S)-homoisocitrate
P20967	KGD1 YIL125W	2-oxoglutarate dehydrogenase, mitochondrial	Enzyme	Coenzyme A NAD NADH Oxoglutaric acid Succinyl-CoA lipoamide S(8)-succinyldihydrolipoamide hydron Carbon dioxide
P32473	PDB1 YBR221C	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial	Enzyme	Coenzyme A NAD NADH Pyruvic acid Acetyl-CoA Thiamine pyrophosphate Carbon dioxide 2-(a-Hydroxyethyl)thiamine diphosphate
P16451	PDX1	Pyruvate dehydrogenase complex protein X component, mitochondrial		Coenzyme A NAD NADH Pyruvic acid Acetyl-CoA Thiamine pyrophosphate Carbon dioxide 2-(a-Hydroxyethyl)thiamine diphosphate
P53157	MPC1	Mitochondrial pyruvate carrier 1	Transporter	Not Available