1651
Pathway
Purine Degradation
Pseudouridine is phosphorylated by interacting with atp and a psuK resulting in the release of an ADP, a hydrogen ion and a pseudouridine 5'-phosphate. The latter compound then reacts with water through a pseudouridine 5'-phosphate glycosidase resulting in the release of a uracil and D-ribofuranose 5-phosphate
Metabolic
PW001887
Center
PathwayVisualizationContext2174
1253
1491
#000099
PathwayVisualization1635
1651
Purine Degradation
Pseudouridine is phosphorylated by interacting with atp and a psuK resulting in the release of an ADP, a hydrogen ion and a pseudouridine 5'-phosphate. The latter compound then reacts with water through a pseudouridine 5'-phosphate glycosidase resulting in the release of a uracil and D-ribofuranose 5-phosphate
Metabolic
3
112381
Endocytosis
SubPathway
111971
613
Compound
3498
4882030
Breitman TR, Scher CD: Growth of pyrimidineless strains of Escherichia coli on 5-ribosyluracil (pseudouridine). J Bacteriol. 1968 Nov;96(5):1873-4.
1651
Pathway
3499
4912525
Breitman TR: Pseudouridulate synthetase of Escherichia coli: correlation of its activity with utilization of pseudouridine for growth. J Bacteriol. 1970 Jul;103(1):263-4.
1651
Pathway
3500
11720289
Del Campo M, Kaya Y, Ofengand J: Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA. 2001 Nov;7(11):1603-15.
1651
Pathway
3501
12581659
Ferre-D'Amare AR: RNA-modifying enzymes. Curr Opin Struct Biol. 2003 Feb;13(1):49-55.
1651
Pathway
3502
9425056
Huang L, Pookanjanatavip M, Gu X, Santi DV: A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophilic catalyst. Biochemistry. 1998 Jan 6;37(1):344-51. doi: 10.1021/bi971874+.
1651
Pathway
3503
18591240
Preumont A, Snoussi K, Stroobant V, Collet JF, Van Schaftingen E: Molecular identification of pseudouridine-metabolizing enzymes. J Biol Chem. 2008 Sep 12;283(37):25238-46. doi: 10.1074/jbc.M804122200. Epub 2008 Jun 30.
1651
Pathway
3504
10428788
Ramamurthy V, Swann SL, Paulson JL, Spedaliere CJ, Mueller EG: Critical aspartic acid residues in pseudouridine synthases. J Biol Chem. 1999 Aug 6;274(32):22225-30.
1651
Pathway
3505
4334133
Solomon LR, Breitman TR: Pseudouridine kinase of escherichia coli: a new enzyme. Biochem Biophys Res Commun. 1971 Jul 16;44(2):299-304.
1651
Pathway
1
Cell
CL:0000000
2
Platelet
CL:0000233
5
Hepatocyte
CL:0000182
3
Neuron
CL:0000540
4
Cardiomyocyte
CL:0000746
8
Beta cell
CL:0000639
7
Epithelial Cell
CL:0000066
1
Homo sapiens
9606
Eukaryote
Human
2
Bacteria
2
Prokaryote
Bacteria
3
Escherichia coli
562
Prokaryote
12
Mus musculus
10090
Eukaryote
Mouse
17
Rattus norvegicus
10116
Eukaryote
Rat
19
Schizosaccharomyces pombe
4896
Eukaryote
24
Solanum lycopersicum
4081
Eukaryote
Tomato
4
Arabidopsis thaliana
3702
Eukaryote
Thale cress
18
Saccharomyces cerevisiae
4932
Eukaryote
Yeast
21
Xenopus laevis
8355
Eukaryote
African clawed frog
6
Caenorhabditis elegans
6239
Eukaryote
Roundworm
25
Escherichia coli (strain K12)
83333
Prokaryote
49
Bathymodiolus platifrons
220390
Eukaryote
Deep sea mussel
23
Pseudomonas aeruginosa
287
Prokaryote
60
Nitzschia sp.
0001
Eukaryote
Nitzschia4
5
Bos taurus
9913
Eukaryote
Cattle
10
Drosophila melanogaster
7227
Eukaryote
Fruit fly
1
Cytosol
GO:0005829
3
Mitochondrial Matrix
GO:0005759
5
Cytoplasm
GO:0005737
14
Mitochondrial Outer Membrane
GO:0005741
2
Mitochondrion
GO:0005739
15
Nucleus
GO:0005634
4
Peroxisome
GO:0005777
13
Endoplasmic Reticulum
GO:0005783
7
Endoplasmic Reticulum Membrane
GO:0005789
10
Cell Membrane
GO:0005886
27
Peroxisome Membrane
GO:0005778
31
Periplasmic Space
GO:0005620
11
Extracellular Space
GO:0005615
35
Chloroplast
GO:0009507
12
Mitochondrial Inner Membrane
GO:0005743
32
Inner Membrane
GO:0070258
19
sarcoplasmic reticulum
GO:0016529
24
Mitochondrial Intermembrane Space
GO:0005758
36
Membrane
GO:0016020
53
Endoplasmic Reticulum Body
GO:0010168
34
Plant-Type Vacuole
GO:0000325
6
Lysosome
GO:0005764
16
Lysosomal Lumen
GO:0043202
18
Melanosome Membrane
GO:0033162
25
Golgi apparatus
GO:0005794
20
Endoplasmic Reticulum Lumen
GO:0005788
21
Synapse
GO:0045202
40
Periplasm
GO:0042597
2
Endothelium
BTO:0000393
1
Liver
BTO:0000759
72
9
7
Nervous System
BTO:0001484
18
Pancreas
BTO:0000988
25
Intestine
BTO:0000648
8
Blood Vessel
BTO:0001102
74
11
28
Stomach
BTO:0001307
155
26
4
Adrenal Medulla
BTO:0000049
71
8
11
Heart
BTO:0000562
73
10
2
1
1
1
PW_BS000002
4
3
1
1
PW_BS000004
8
5
1
1
PW_BS000008
16
2
1
2
PW_BS000016
22
14
1
1
PW_BS000022
13
1
2
1
PW_BS000013
32
1
15
1
5
PW_BS000032
5
4
1
1
PW_BS000005
39
7
1
1
3
PW_BS000039
3
2
1
1
PW_BS000003
18
13
1
1
PW_BS000018
10
1
7
1
1
PW_BS000010
49
7
1
1
PW_BS000049
14
10
1
PW_BS000014
58
1
14
1
1
PW_BS000058
59
27
1
1
PW_BS000059
27
15
1
PW_BS000027
46
1
1
4
PW_BS000046
29
1
1
1
PW_BS000029
66
18
5
1
8
PW_BS000066
72
5
1
3
PW_BS000072
61
25
1
7
PW_BS000061
51
8
1
PW_BS000051
23
15
1
1
PW_BS000023
31
1
5
1
1
PW_BS000031
91
8
5
1
1
PW_BS000091
54
1
3
1
5
PW_BS000054
89
2
PW_BS000089
26
1
1
1
5
PW_BS000026
7
1
1
PW_BS000007
97
1
5
2
1
PW_BS000097
100
5
2
1
PW_BS000100
104
14
3
1
PW_BS000104
101
5
3
1
PW_BS000101
111
5
12
1
PW_BS000111
112
2
12
1
PW_BS000112
103
3
3
1
PW_BS000103
117
1
3
1
PW_BS000117
118
1
17
1
PW_BS000118
120
3
17
1
PW_BS000120
129
1
5
12
1
PW_BS000129
132
1
12
1
PW_BS000132
133
3
12
1
PW_BS000133
135
5
17
1
PW_BS000135
108
1
3
PW_BS000108
143
1
5
19
1
PW_BS000143
146
5
19
1
PW_BS000146
107
31
3
PW_BS000107
147
1
24
1
PW_BS000147
151
1
4
1
PW_BS000151
155
3
24
1
PW_BS000155
161
3
18
1
PW_BS000161
166
1
1
PW_BS000166
178
3
21
1
PW_BS000178
188
1
18
PW_BS000024
160
1
18
1
PW_BS000160
199
14
18
1
PW_BS000024
205
5
6
1
PW_BS000024
206
2
6
1
PW_BS000024
210
13
18
1
PW_BS000024
213
7
18
1
PW_BS000024
211
10
18
PW_BS000024
198
5
18
1
PW_BS000024
216
4
18
1
PW_BS000024
217
15
18
PW_BS000024
218
15
18
1
PW_BS000024
163
2
18
1
PW_BS000163
222
3
4
1
PW_BS000024
190
11
18
PW_BS000024
225
35
4
1
PW_BS000024
277
1
2
18
PW_BS000024
170
18
PW_BS000170
281
1
25
1
PW_BS000024
164
4
PW_BS000164
285
10
4
1
PW_BS000024
226
4
4
1
PW_BS000024
290
5
49
1
PW_BS000024
223
12
4
1
PW_BS000024
308
10
1
1
PW_BS000024
315
1
23
PW_BS000024
322
1
23
1
PW_BS000024
318
31
23
PW_BS000024
253
5
4
1
PW_BS000024
134
12
12
1
PW_BS000134
329
14
12
1
PW_BS000028
333
1
2
12
PW_BS000028
336
1
12
1
PW_BS000028
332
1
7
12
1
PW_BS000028
350
1
14
12
1
PW_BS000028
128
15
12
1
PW_BS000128
351
15
12
PW_BS000028
353
25
12
7
PW_BS000028
335
27
12
1
PW_BS000028
115
10
12
PW_BS000115
130
13
12
1
PW_BS000130
331
7
12
1
PW_BS000028
334
4
12
1
PW_BS000028
368
3
60
1
PW_BS000028
184
1
2
1
PW_BS000024
119
2
17
1
PW_BS000119
1
1
PW_BS000001
124
1
5
1
PW_BS000124
94
3
PW_BS000094
388
1
6
1
PW_BS000112
109
32
3
PW_BS000109
122
5
5
1
PW_BS000122
406
3
5
1
PW_BS000115
407
2
5
1
PW_BS000115
382
14
5
1
PW_BS000100
412
1
2
5
PW_BS000115
429
1
5
1
PW_BS000115
123
1
7
5
1
PW_BS000123
433
1
14
5
1
PW_BS000115
408
4
5
1
PW_BS000115
410
15
5
1
PW_BS000115
125
13
5
1
PW_BS000125
383
7
5
1
PW_BS000100
405
10
5
PW_BS000115
422
27
5
1
PW_BS000115
435
15
5
PW_BS000115
399
14
17
1
PW_BS000113
446
1
2
17
PW_BS000115
464
1
17
1
PW_BS000115
447
1
7
17
1
PW_BS000115
468
1
14
17
1
PW_BS000115
374
4
17
1
PW_BS000053
444
15
17
1
PW_BS000115
136
13
17
1
PW_BS000136
398
7
17
1
PW_BS000113
376
10
17
PW_BS000053
472
25
17
7
PW_BS000115
375
27
17
1
PW_BS000053
470
15
17
PW_BS000115
297
5
10
1
PW_BS000024
479
3
10
1
PW_BS000115
299
1
10
1
PW_BS000024
481
2
10
1
PW_BS000115
484
14
10
1
PW_BS000115
485
15
10
1
PW_BS000115
300
13
10
1
PW_BS000024
495
7
10
1
PW_BS000115
478
10
10
PW_BS000115
491
27
10
1
PW_BS000115
499
15
10
PW_BS000115
501
3
6
1
PW_BS000115
389
14
6
1
PW_BS000112
516
15
6
1
PW_BS000115
395
13
6
1
PW_BS000113
390
7
6
1
PW_BS000112
209
10
6
PW_BS000024
508
27
6
1
PW_BS000115
517
15
6
PW_BS000115
15
11
1
PW_BS000015
47
19
1
4
PW_BS000047
313
23
PW_BS000024
17
12
1
1
PW_BS000017
42
24
1
1
PW_BS000042
70
28
5
1
1
PW_BS000070
105
11
3
PW_BS000105
157
2
24
1
PW_BS000157
159
24
PW_BS000159
152
8
4
PW_BS000152
187
31
18
PW_BS000024
219
31
4
PW_BS000024
220
1
4
PW_BS000024
212
1
7
18
1
PW_BS000024
162
12
18
1
PW_BS000162
224
2
4
1
PW_BS000024
195
13
18
PW_BS000024
249
13
4
1
PW_BS000024
286
36
4
1
PW_BS000024
287
53
4
1
PW_BS000024
227
34
4
1
PW_BS000024
294
11
4
1
PW_BS000024
312
5
23
1
PW_BS000024
320
11
23
PW_BS000024
293
4
1
PW_BS000024
114
11
12
PW_BS000114
327
1
1
12
5
PW_BS000028
347
1
3
12
5
PW_BS000028
345
24
12
1
PW_BS000028
310
31
2
PW_BS000024
304
1
2
PW_BS000024
409
11
5
PW_BS000115
424
1
1
5
5
PW_BS000115
425
1
3
5
5
PW_BS000115
418
24
5
1
PW_BS000115
384
12
5
1
PW_BS000100
137
11
17
PW_BS000137
459
1
1
17
5
PW_BS000115
460
1
3
17
5
PW_BS000115
454
24
17
1
PW_BS000115
121
12
17
1
PW_BS000121
483
11
10
PW_BS000115
489
24
10
1
PW_BS000115
480
12
10
1
PW_BS000115
208
11
6
PW_BS000024
506
24
6
1
PW_BS000115
391
12
6
1
PW_BS000112
9
6
1
1
PW_BS000009
28
1
16
1
1
PW_BS000028
20
4
1
1
1
PW_BS000020
33
18
1
1
PW_BS000033
43
25
1
1
PW_BS000043
24
4
10
1
1
PW_BS000024
60
25
1
PW_BS000060
36
1
20
1
1
PW_BS000036
37
7
21
1
3
PW_BS000037
93
25
20
1
1
PW_BS000093
113
6
12
1
PW_BS000113
110
2
3
1
PW_BS000110
126
6
5
1
PW_BS000126
127
1
16
5
1
PW_BS000127
6
1
3
1
PW_BS000006
140
10
3
PW_BS000140
95
1
7
2
1
PW_BS000095
180
2
21
1
PW_BS000180
207
6
6
1
PW_BS000024
214
25
18
1
PW_BS000024
215
6
18
1
PW_BS000024
65
11
1
PW_BS000065
291
6
49
1
PW_BS000024
292
4
49
1
PW_BS000024
298
1
7
10
1
PW_BS000024
301
6
10
1
PW_BS000024
302
1
16
10
1
PW_BS000024
337
1
16
12
1
PW_BS000028
341
4
1
12
1
PW_BS000028
343
18
12
1
PW_BS000028
352
25
12
PW_BS000028
356
25
12
1
PW_BS000028
360
4
10
12
1
PW_BS000028
370
2
60
1
PW_BS000028
228
36
1
PW_BS000024
232
40
3
PW_BS000024
415
18
5
1
PW_BS000115
414
1
5
5
1
PW_BS000115
419
25
5
1
PW_BS000115
434
4
10
5
1
PW_BS000115
436
25
5
PW_BS000115
443
6
17
1
PW_BS000115
448
1
16
17
1
PW_BS000115
451
18
17
1
PW_BS000115
450
1
5
17
1
PW_BS000115
455
25
17
1
PW_BS000115
469
4
10
17
1
PW_BS000115
471
25
17
PW_BS000115
482
4
10
1
PW_BS000115
487
18
10
1
PW_BS000115
490
25
10
1
PW_BS000115
502
4
6
1
PW_BS000115
504
18
6
1
PW_BS000115
507
25
6
1
PW_BS000115
515
4
10
6
1
PW_BS000115
513
1
7
6
1
PW_BS000115
613
Pseudouridine
HMDB0000767
Pseudouridine is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. Pseudouridine is found in all species and in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA (Wikipedia).
1445-07-4
C02067
15047
17802
14319
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=O
C9H12N2O6
InChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1
PTJWIQPHWPFNBW-GBNDHIKLSA-N
5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
244.2014
244.069536126
-0.58
5
β-pseudouridine
0
0
FDB014724
5-(b-d-ribofuranosyl)uracil;5-(b-delta-ribofuranosyl)uracil;5-ribosyluracil;5-b-d-ribofuranosyl-uracil;5-beta-delta-ribofuranosyl-uracil;Pseudouridine;Pseudouridine c;B-d-pseudouridine;B-pseudouridine;Beta-pseudouridine;Beta-delta-pseudouridine;Y-uridine;(1s)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-d-ribitol;5-(beta-d-ribofuranosyl)uracil;P;Psi-uridine;5-(β-d-ribofuranosyl)uracil;β-pseudouridine
PW_C000613
Q
414
Adenosine triphosphate
HMDB0000538
Adenosine triphosphate (ATP) is a nucleotide consisting of a purine base (adenine) attached to the first carbon atom of ribose (a pentose sugar). Three phosphate groups are esterified at the fifth carbon atom of the ribose. ATP is incorporated into nucleic acids by polymerases in the processes of DNA replication and transcription. ATP contributes to cellular energy charge and participates in overall energy balance, maintaining cellular homeostasis. ATP can act as an extracellular signaling molecule via interactions with specific purinergic receptors to mediate a wide variety of processes as diverse as neurotransmission, inflammation, apoptosis, and bone remodelling. Extracellular ATP and its metabolite adenosine have also been shown to exert a variety of effects on nearly every cell type in human skin, and ATP seems to play a direct role in triggering skin inflammatory, regenerative, and fibrotic responses to mechanical injury, an indirect role in melanocyte proliferation and apoptosis, and a complex role in Langerhans cell-directed adaptive immunity. During exercise, intracellular homeostasis depends on the matching of adenosine triphosphate (ATP) supply and ATP demand. Metabolites play a useful role in communicating the extent of ATP demand to the metabolic supply pathways. Effects as different as proliferation or differentiation, chemotaxis, release of cytokines or lysosomal constituents, and generation of reactive oxygen or nitrogen species are elicited upon stimulation of blood cells with extracellular ATP. The increased concentration of adenosine triphosphate (ATP) in erythrocytes from patients with chronic renal failure (CRF) has been observed in many studies but the mechanism leading to these abnormalities still is controversial. (PMID: 15490415, 15129319, 14707763, 14696970, 11157473).
56-65-5
C00002
5957
15422
ATP
5742
DB00171
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
C10H16N5O13P3
InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
({[({[(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
507.181
506.995745159
-2.05
7
adenosine triphosphate
0
-3
FDB021813
5'-(tetrahydrogen triphosphate) adenosine;5'-atp;Atp;Adenosine 5'-triphosphate;Adenosine 5'-triphosphorate;Adenosine 5'-triphosphoric acid;Adenosine triphosphate;Adenylpyrophosphorate;Adenylpyrophosphoric acid;Adephos;Adetol;Adynol;Atipi;Atriphos;Cardenosine;Fosfobion;Glucobasin;Myotriphos;Phosphobion;Striadyne;Triadenyl;Triphosphaden;Triphosphoric acid adenosine ester;Adenosine-5'-triphosphate;H4atp;Adenosine triphosphoric acid;Adenosine-5'-triphosphoric acid
PW_C000414
ATP
9
2
21
4
60
8
266
16
414
22
478
13
733
32
799
5
934
39
976
3
2105
18
2112
10
2146
49
2156
14
2160
58
2405
59
2434
27
2726
46
2812
29
3029
66
3163
72
3616
61
3617
51
4399
23
4474
31
4768
91
4864
54
5032
89
5035
26
5155
7
5205
97
5215
100
5250
104
5291
101
5313
111
5346
112
5390
103
5406
117
5430
118
5443
120
5542
129
5556
132
5569
133
5603
135
5621
108
5846
143
5854
146
5876
107
5897
147
5924
151
6048
155
6109
161
6230
166
6493
178
6839
188
6870
160
6976
199
7157
205
7184
206
7209
210
7225
213
7229
211
7298
198
7302
216
7390
217
7408
218
7432
163
7481
222
7499
190
8186
225
11847
277
11903
170
12010
281
12039
164
12178
285
12578
226
12691
290
13264
223
15327
308
42326
315
42621
322
42694
318
77028
253
77218
134
77233
329
77468
333
77632
336
78037
332
78041
350
78168
128
78214
351
78240
353
78411
335
78494
115
78850
130
78865
331
78919
334
80028
368
80046
184
80674
119
85629
1
94826
124
113234
94
113282
388
116280
109
119914
122
119992
406
120154
407
120245
382
120362
412
121246
429
121392
123
121397
433
121471
408
121974
410
122065
125
122079
383
122083
405
122402
422
122444
435
122919
399
123009
446
123816
464
123951
447
123956
468
124029
374
124527
444
124616
136
124630
398
124634
376
124943
472
124972
375
125011
470
125304
297
125371
479
125392
299
125515
481
125595
484
126123
485
126220
300
126234
495
126240
478
126547
491
126596
499
126913
501
127123
389
127731
516
127781
395
127796
390
127801
209
128119
508
128167
517
984
Pseudouridine 5'-phosphate
HMDB0001271
Pseudouridine (5-ribosyluracil) is a ubiquitous yet enigmatic constituent of structural RNAs (transfer, ribosomal, small nuclear, and small nucleolar). Although pseudouridine (psi) was the first modified nucleoside to be discovered in RNA, and is the most abundant, its biosynthesis and biological roles have remained poorly understood since its identification as a "fifth nucleoside" in RNA. Recently, a combination of biochemical, biophysical, and genetic approaches has helped to illuminate the structural consequences of psi in polyribonucleotides, the biochemical mechanism of U-->psi isomerization in RNA, and the role of modification enzymes (psi synthases) and box H/ACA snoRNAs, a class of eukaryotic small nucleolar RNAs, in the site-specific biosynthesis of psi. Through its unique ability to coordinate a structural water molecule via its free N1-H, psi exerts a subtle but significant "rigidifying" influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most (but perhaps not all) of the psi residues in RNA. Certain genetic mutants lacking specific psi residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. In particular, normal growth is severely compromised in an Escherichia coli mutant deficient in a pseudouridine synthase responsible for the formation of three closely spaced psi residues in the mRNA decoding region of the 23S rRNA. Such studies demonstrate that pseudouridylation of RNA confers an important selective advantage in a natural biological context. PMID: 10902565.
1157-60-4
C01168
439424
18116
PSEUDOURIDINE-5-P
388535
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O
C9H13N2O9P
InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
MOBMOJGXNHLLIR-GBNDHIKLSA-N
{[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid
324.1813
324.035866536
-1.64
6
pseudouridine 5'-phosphate
0
-2
FDB022525
Pseudouridine 5'-phosphate;(1s)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol;5-(5-o-phosphono-beta-d-ribofuranosyl)pyrimidine-2,4(1h,3h)-dione;Pseudouridine 5'-phosphoric acid;5-(5-o-phosphono-b-d-ribofuranosyl)pyrimidine-2,4(1h,3h)-dione;5-(5-o-phosphono-β-d-ribofuranosyl)pyrimidine-2,4(1h,3h)-dione
PW_C000984
Psed-5P
1034
Adenosine diphosphate
HMDB0001341
Adenosine diphosphate, abbreviated ADP, is a nucleotide. It is an ester of pyrophosphoric acid with the nucleotide adenine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine. ADP is the product of ATP dephosphorylation by ATPases. ADP is converted back to ATP by ATP synthases.
58-64-0
C00008
6022
16761
ADP
5800
NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(O)(=O)OP(O)(O)=O)[C@@H](O)[C@H]1O
C10H15N5O10P2
InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
XTWYTFMLZFPYCI-KQYNXXCUSA-N
[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid
427.2011
427.029414749
-2.12
6
adenosine-diphosphate
0
-2
FDB021817
Adp;Adenosindiphosphorsaeure;Adenosine 5'-pyrophosphate;Adenosine diphosphate;Adenosine pyrophosphate;Adenosine-5'-diphosphate;Adenosine-5-diphosphate;Adenosine-diphosphate;5'-adenylphosphoric acid;Adenosine 5'-diphosphate;H3adp;5'-adenylphosphate;Adenosine 5'-diphosphoric acid;Adenosine-5'-diphosphoric acid
PW_C001034
ADP
23
4
134
8
415
22
482
13
801
5
963
15
978
3
1061
14
1518
2
1901
49
2104
18
2113
10
2161
58
2408
59
2435
27
2728
47
2736
46
2855
29
3165
72
3635
61
4400
23
4476
31
4770
91
5036
26
5157
7
5208
97
5217
100
5315
111
5349
112
5392
103
5446
120
5544
129
5572
133
5624
108
5741
117
5764
101
5849
143
5856
146
5878
107
5899
147
5926
151
6050
155
6111
161
6231
166
6495
178
6700
94
6841
188
6872
160
7159
205
7187
206
7208
210
7226
213
7231
211
7300
198
7303
216
7391
217
7410
218
7433
163
7483
222
8187
225
11851
277
11905
170
12013
281
12180
285
13262
223
15329
308
42328
315
42398
313
42622
322
42696
318
77029
253
77087
132
77216
134
77306
329
77472
333
77663
336
78039
332
78043
350
78170
128
78215
351
78244
353
78414
335
78495
115
78705
331
78849
130
78920
334
80030
368
80622
118
80651
135
80676
119
94827
124
113283
388
116204
109
119944
122
119994
406
120156
407
120318
382
120366
412
121248
429
121394
123
121399
433
121472
408
121899
383
121976
410
122064
125
122085
405
122405
422
122445
435
122973
399
123013
446
123818
464
123953
447
123958
468
124030
374
124452
398
124529
444
124615
136
124636
376
124947
472
124975
375
125012
470
125334
297
125373
479
125492
299
125517
481
125645
484
126125
485
126219
300
126235
495
126242
478
126550
491
126597
499
126915
501
127733
516
127780
395
127797
390
127803
209
128122
508
128168
517
128313
389
40034
Hydrogen Ion
HMDB0059597
Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions. Under aqueous conditions found in biochemistry, hydrogen ions exist as the hydrated form hydronium, H3O+, but these are often still referred to as hydrogen ions or even protons by biochemists. [WikiPedia])
C00080
1038
15378
1010
[H+]
H
InChI=1S/p+1
GPRLSGONYQIRFK-UHFFFAOYSA-N
hydron
1.0079
1.007825032
0
hydron
1
0
H+;H(+);Hydrogen cation;Hydron;Proton
PW_C040034
H+
215
4
670
8
753
15
788
31
848
3
1116
2
1463
26
1464
54
2231
49
2780
17
4250
22
4254
42
4547
10
4576
18
4694
70
5241
103
5327
111
5353
112
5626
108
5639
107
5699
100
5720
105
5742
117
5963
147
6037
155
6070
157
6093
161
6130
159
6232
166
6483
178
6601
152
6692
101
6843
188
6910
187
7100
163
7168
205
7191
206
7453
219
7454
220
7472
222
7525
213
7532
210
7558
212
7572
160
7590
170
8195
225
8218
151
8243
226
8413
162
8420
224
9139
195
9155
249
11915
164
12015
281
12181
285
12246
286
12266
287
12521
227
13257
223
13325
294
15330
308
42329
315
42354
318
42401
322
42405
312
42454
320
76912
293
77136
133
77210
134
77372
331
77804
114
77955
132
77990
327
77991
347
78379
345
79929
130
80019
368
80387
310
80388
304
80722
119
93823
124
94823
383
110550
388
112855
94
113280
390
115537
398
115539
118
115856
336
116205
109
119973
406
120193
407
120549
122
120593
409
121170
424
121171
425
122569
418
122615
384
122687
125
122758
120
123183
135
123218
137
123742
459
123743
460
125141
454
125188
121
125273
136
125359
479
125550
481
125730
483
125736
297
125809
299
126517
495
126717
489
126766
480
126823
300
126902
501
127213
208
128308
506
128361
391
128430
395
1420
Water
HMDB0002111
Water is a chemical substance that is essential to all known forms of life. It appears colorless to the naked eye in small quantities, though it is actually slightly blue in color. It covers 71% of Earth's surface. Current estimates suggest that there are 1.4 billion cubic kilometers (330 million m3) of it available on Earth, and it exists in many forms. It appears mostly in the oceans (saltwater) and polar ice caps, but it is also present as clouds, rain water, rivers, freshwater aquifers, lakes, and sea ice. Water in these bodies perpetually moves through a cycle of evaporation, precipitation, and runoff to the sea. Clean water is essential to human life. In many parts of the world, it is in short supply. From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the body's solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Water is thus essential and central to these metabolic processes. Water is also central to photosynthesis and respiration. Photosynthetic cells use the sun's energy to split off water's hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the sun's energy and reform water and CO2 in the process (cellular respiration). Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH-) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7. Stomach acid (HCl) is useful to digestion. However, its corrosive effect on the esophagus during reflux can temporarily be neutralized by ingestion of a base such as aluminum hydroxide to produce the neutral molecules water and the salt aluminum chloride. Human biochemistry that involves enzymes usually performs optimally around a biologically neutral pH of 7.4. (Wikipedia).
7732-18-5
C00001
962
15377
937
O
H2O
InChI=1S/H2O/h1H2
XLYOFNOQVPJJNP-UHFFFAOYSA-N
water
18.0153
18.010564686
1
water
0
0
FDB013390
Dihydrogen oxide;Steam;[oh2];Acqua;Agua;Aqua;Bound water;Dihydridooxygen;Eau;H2o;Hoh;Hydrogen hydroxide;Wasser
PW_C001420
H2O
55
8
94
9
109
5
139
4
151
3
162
14
481
13
526
15
624
28
652
10
691
20
770
33
823
18
838
2
1094
31
1377
49
1465
54
1590
43
2018
24
2532
22
2678
60
2727
46
2778
17
2805
29
3143
70
3164
72
3634
61
4598
36
4727
37
4941
93
5030
27
5156
7
5195
97
5214
100
5227
94
5236
103
5297
105
5319
111
5343
113
5355
112
5402
110
5470
123
5483
125
5492
126
5507
127
5534
130
5537
114
5541
129
5591
135
5608
118
5622
108
5691
6
5759
140
5778
101
5841
143
5853
146
5877
107
5890
95
5910
147
5940
151
6032
155
6059
157
6087
161
6123
163
6133
159
6215
1
6218
166
6477
178
6507
180
6600
152
6713
117
6840
188
6888
160
7162
205
7181
207
7193
206
7211
211
7228
213
7238
214
7243
215
7295
198
7350
216
7388
210
7401
212
7467
222
7492
224
7500
190
7588
170
8201
225
8237
226
8414
162
9265
26
11850
277
11922
164
12011
281
12213
285
12250
286
12264
287
12327
249
12520
227
12632
65
12693
290
12705
291
12715
292
13007
298
13019
300
13025
301
13037
302
13261
223
13327
294
15340
308
42327
315
42695
318
43691
322
76914
293
77019
253
77102
132
77131
133
77215
134
77378
331
77397
332
77471
333
77516
115
77536
334
77628
336
77722
337
77759
341
77816
343
77982
347
78071
329
78235
352
78242
353
78270
356
79113
360
80014
368
80039
370
80591
228
80656
119
93830
383
94794
384
110557
390
110639
391
115844
398
119879
232
119915
122
119963
406
120008
407
120046
408
120113
124
120365
412
120430
405
120438
409
120606
415
120794
414
121158
425
121240
429
121351
121
121381
419
121607
434
122118
382
122384
436
122753
120
122797
374
122804
443
123012
446
123064
376
123072
137
123131
447
123142
136
123162
448
123231
451
123384
450
123730
460
123810
464
123940
455
124165
469
124670
399
124938
471
124945
472
125305
297
125353
479
125386
481
125424
482
125480
299
125682
483
125707
478
125745
487
126054
490
126238
495
126273
484
126764
480
126896
501
126963
502
127017
388
127177
208
127199
209
127227
504
127506
507
127576
515
127836
389
128082
395
128176
513
204
Uracil
HMDB0000300
Uracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. UDP and UTP regulate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose in the liver and other tissues in the process of carbohydrate metabolism. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes.
66-22-8
C00106
1174
17568
URACIL
1141
DB03419
O=C1NC=CC(=O)N1
C4H4N2O2
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
ISAKRJDGNUQOIC-UHFFFAOYSA-N
1,2,3,4-tetrahydropyrimidine-2,4-dione
112.0868
112.027277382
-0.63
2
uracil
0
0
FDB006426
2,4-dihydroxypyrimidine;2,4-dioxopyrimidine;2,4-pyrimidinediol;2,4-pyrimidinedione;Hybar x;Pirod;Pyrod;Uracil;Sq-8493sid51088798;Sq-6201sq-7726sid70371;Bms-205603-01uracil
PW_C000204
Uracil
538
8
2741
2
77589
111
78739
132
120451
122
122220
124
123085
135
124772
118
125695
297
126383
299
127189
205
127943
388
40975
D-ribofuranose 5-phosphate
D-Ribofuranose 5-phosphate belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups. D-Ribofuranose 5-phosphate is soluble (in water) and a moderately acidic compound (based on its pKa). D-Ribofuranose 5-phosphate may be a unique E.coli metabolite.
52742
OC1OC(COP([O-])([O-])=O)C(O)C1O
C5H9O8P
InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/p-2
KTVPXOYAKDPRHY-UHFFFAOYSA-L
(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate
228.094
228.004601408
-0.46
3
(3,4,5-trihydroxyoxolan-2-yl)methyl phosphate
-2
-2
PW_C040975
D-Rf5P
7637
Pseudouridine kinase
P30235
Carbohydrate transport and metabolism. Catalyzes the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (PsiMP).
psuK
U00096
3
2.7.1.83
7567
Pseudouridine-5'-phosphate glycosidase
P33025
Catalyzes the hydrolysis of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. In vitro, can also catalyze the reverse reaction.
Catalyzes the hydrolysis of pseudouridine 5'-phosphate (PsiMP) to ribose 5-phosphate and uracil. In vitro, can also catalyze the reverse reaction..
psuG
b2165
3
4.2.1.70
3878
pseudouridine kinase
3
PW_P003878
10823
7637
3879
predicted pseudouridine 5'-phosphate glycosidase
3
PW_P003879
10824
7567
5150
false
PW_R005150
Right
20824
613
1
Compound
false
20825
414
1
Compound
false
20826
984
1
Compound
false
20827
1034
1
Compound
false
20828
40034
1
Compound
false
5123
3878
2.7.1.83
5151
false
PW_R005151
Right
20829
984
1
Compound
false
20830
1420
1
Compound
false
20831
204
1
Compound
false
20832
40975
1
Compound
false
5124
3879
4.2.1.70
61433
613
3
false
331
365
10
regular
100
100
61434
414
42
false
491
460
10
regular
50
30
61435
984
3
false
921
361
10
regular
100
110
61436
1034
43
false
821
501
10
regular
50
30
61437
40034
55
false
792
291
10
regular
78
78
61438
1420
49
false
1012
518
10
regular
78
78
61439
204
3
false
1026
731
10
regular
100
100
61440
40975
3
false
921
851
10
regular
100
110
28622
7637
2
false
596
383
8
subunit
regular
150
70
28623
7567
2
false
896
629
8
subunit
regular
150
70
24106
3878
1635
28310
28622
24107
3879
1635
28311
28623
88222
M431.33333333333337 417 C473.33333333333337 417 546.3333333333334 418 596.3333333333334 418
5
false
18
88223
M516.3333333333334 460 C517.3333333333334 426 545.3333333333334 417 596.3333333333334 418
5
false
18
88224
M921.3333333333334 419 C882.3333333333334 418 786.3333333333334 419 746.3333333333334 418
5
false
18
true
M 25.946855044164835 13.26155629629604 L 11 12 L 17.380887721185843 25.575134323078345
false
88225
M846.3333333333334 501 C847.3333333333334 433 820.3333333333334 419 746.3333333333334 418
5
false
18
true
M 25.946855044164835 13.26155629629604 L 11 12 L 17.380887721185843 25.575134323078345
false
88226
M831.3333333333334 369 C831.3333333333334 413 786.3333333333334 419 746.3333333333334 418
5
false
18
true
M 25.946855044164835 13.26155629629604 L 11 12 L 17.380887721185843 25.575134323078345
false
88227
M971.3333333333334 471 C971.3333333333334 519 971.3333333333334 562 971.3333333333334 629
5
false
18
88228
M1012.3333333333334 557 C982.3333333333334 557 971.3333333333334 581 971.3333333333334 629
5
false
18
88229
M1026.3333333333335 781 C991.3333333333334 782 970.3333333333334 768 971.3333333333334 699
5
false
18
true
M 25.946855044164835 13.26155629629604 L 11 12 L 17.380887721185843 25.575134323078345
false
88230
M971.3333333333334 851 C972.3333333333334 766 969.3333333333334 777 971.3333333333334 699
5
false
18
true
M 25.946855044164835 13.26155629629604 L 11 12 L 17.380887721185843 25.575134323078345
false
3775336
M381 465 C381 495 381 500 381 530
5
false
18
17935
1635
5150
69028
61433
88222
Left
69029
61434
88223
Left
69030
61435
88224
Right
69031
61436
88225
Right
69032
61437
88226
Right
18138
5123
24106
17936
1635
5151
69033
61435
88227
Left
69034
61438
88228
Left
69035
61439
88229
Right
69036
61440
88230
Right
18139
5124
24107
112094
112381
1635
217
false
306
530
16
regular
108732
61433
3775336
Right
186401
491
531
0.8
0.8
0
2
92
479
481
3190
M125 225 C125 175 175 125 225 125 C528 125 922.9999999999999 125 1226 125 C1276 125 1326 175 1326 225 C1326 468 1326 785 1326 1028 C1326 1078 1276 1128 1226 1128 C922.9999999999999 1128 528 1128 225 1128 C175 1128 125 1078 125 1028 C125 785 125 468 125 225
1
true
6
1201.0
1003.0
3191
M225.33333333333337 326 C225.33333333333337 276 275.33333333333337 226 325.33333333333337 226 C567.3333333333334 226 882.3333333333334 226 1124.3333333333335 226 C1174.3333333333335 226 1224.3333333333335 276 1224.3333333333335 326 C1224.3333333333335 508 1224.3333333333335 746 1224.3333333333335 928 C1224.3333333333335 978 1174.3333333333335 1028 1124.3333333333335 1028 C882.3333333333334 1028 567.3333333333334 1028 325.33333333333337 1028 C275.33333333333337 1028 225.33333333333337 978 225.33333333333337 928 C225.33333333333337 746 225.33333333333337 508 225.33333333333337 326
1
true
6
0.0
0.0