MiMeDB: Showing metabocard for 5-Phosphoribosylamine (MMDBc0029566)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:32:33 UTC

Update Date

2024-04-30 19:38:05 UTC

Metabolite ID

MMDBc0029566

Metabolite Identification

Common Name

5-Phosphoribosylamine

Description

5-Phosphoribosylamine is a substrate for Amidophosphoribosyltransferase and Trifunctional purine biosynthetic protein adenosine-3.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv0541 02231218562D          

 14 14  0  0  1  0            999 V2000
   -1.5779    0.9195    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7493    0.9158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3991    0.9195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5742    1.7406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5817    0.0946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5827    0.1097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2006   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4502   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8590    0.3329    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2752   -0.9346    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0379   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5326   -0.1476    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7596   -1.5969    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4255    0.3179    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
 10 13  1  6  0  0  0
 12 14  1  1  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029566

> <DATABASE_NAME>
MIME

> <SMILES>
N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
SKCBPEVYGOQGJN-TXICZTDVSA-N

> <FORMULA>
C5H12NO7P

> <MOLECULAR_WEIGHT>
229.125

> <EXACT_MASS>
229.035138255

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.663161093312503

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-2.39

> <JCHEM_LOGP>
-3.545345242649598

> <ALOGPS_LOGS>
-0.78

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.243630161593156

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2256230940421675

> <JCHEM_PKA_STRONGEST_BASIC>
8.000221098750375

> <JCHEM_POLAR_SURFACE_AREA>
142.47

> <JCHEM_REFRACTIVITY>
42.491299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-phospho-β-D-ribosylamine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  P   UNK     0      -2.945   1.716   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      -1.399   1.709   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -4.478   1.716   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -2.939   3.249   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.953   0.177   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.088   0.205   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.374  -0.276   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.840  -1.745   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.603   0.621   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.380  -1.745   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.071  -2.981   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.861  -0.276   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.285  -2.981   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0       4.528   0.593   0.000  0.00  0.00           N+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10   11                                                  
CONECT    9    7   12                                                       
CONECT   10    8   13   12                                                  
CONECT   11    8                                                            
CONECT   12    9   14   10                                                  
CONECT   13   10                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

Synonyms

Value	Source
5-Phospho-D-ribosylamine	ChEBI
5-Phosphoribosyl-1-amine	ChEBI
5-Phospho-beta-D-ribosylamine	Kegg
5-Phospho-b-D-ribosylamine	Generator
5-Phospho-β-D-ribosylamine	Generator
5-P-beta-D-Ribosyl-amine	HMDB
5-Phospho-beta-D-ribosyl-amine	HMDB
PRA	HMDB
Phosphoribosyl-1-amine	HMDB
Phosphoribosylamine	HMDB
beta-Phosphoribosyl-1-amine	HMDB
β-Phosphoribosyl-1-amine	HMDB

Molecular Formula

C₅H₁₂NO₇P

Average Mass

229.125

Monoisotopic Mass

229.035138255

IUPAC Name

{[(2R,3S,4R,5R)-5-amino-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

5-phospho-β-D-ribosylamine

CAS Registry Number

Not Available

SMILES

N[C@@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C5H12NO7P/c6-5-4(8)3(7)2(13-5)1-12-14(9,10)11/h2-5,7-8H,1,6H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1

InChI Key

SKCBPEVYGOQGJN-TXICZTDVSA-N

Chemical Taxonomy

Description

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Secondary alcohol
1,2-diol
Hemiaminal
Organoheterocyclic compound
Oxacycle
Alcohol
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organic nitrogen compound
Primary aliphatic amine
Hydrocarbon derivative
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

5-phospho-D-ribosylamine (CHEBI:37737 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	38.2 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-3.5	ChemAxon
logS	-0.78	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	142.47 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	42.49 m³·mol⁻¹	ChemAxon
Polarizability	18.66 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-002b-9200000000-1c4fff9bc3c106e53faa	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-03dj-9741000000-81d2b48c346eaf5bd609	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-2490000000-890344ea8a2dc31a68cd	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01q9-8950000000-3968c4c6838390005385	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0007-9100000000-696f573fba92b8542f35	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9040000000-95218a5e49093dd3dec6	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-909c9da9ed8687627fbe	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-d063b8fd7634dcdf6580	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03e9-0900000000-a28a2870d14f9b514efa	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03yi-2900000000-3f959957fd3503d8f28b	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052b-9000000000-69bd1484fc7665f256af	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-8090000000-2ebfcb2a817d0e5198a2	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-24	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191999	Trifunctional purine biosynthetic protein adenosine-3	Enzyme	P22102	Homo sapiens
MMDBp0192000	Amidophosphoribosyltransferase	Unknown	Q06203	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0001986	Glycine	Glycineamideribotide	phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase	VMH; KEGG	30371894
MMDBr0007542	Glycine	Glycineamideribotide	Not Available	VMH	30371894
MMDBr0007833	L-Glutamine	L-Glutamic acid	Not Available	VMH; KEGG	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	214	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Chicken	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	409	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria	Actinobacteria	136	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	3	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Aquificae	1
Archaea/Archaea	Euryarchaeota	22		Metabolic reconstruction
Bacteria	Chlorobi	1
Eukaryota/Fungi	Basidiomycota	1
Bacteria	Deinococcus-thermus	1
Bacteria	Cyanobacteria	2
Eukaryota/Fungi	Ascomycota	6	Human feces; Human saliva	Unknown
Bacteria	nah	1
Bacteria	Thermotogae	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001128

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

5-P-BETA-D-RIBOSYL-AMINE

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

37737

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Kamal MA, Christopherson RI: Accumulation of 5-phosphoribosyl-1-pyrophosphate in human CCRF-CEM leukaemia cells treated with antifolates. Int J Biochem Cell Biol. 2004 Mar;36(3):545-51. doi: 10.1016/j.biocel.2003.08.014. [PubMed:14687931 ]

Showing metabocard for 5-Phosphoribosylamine (MMDBc0029566)

MOL for #<Metabolite:0x00007fecfdb4c688>

3D MOL for #<Metabolite:0x00007fecfdb4c688>

3D SDF for #<Metabolite:0x00007fecfdb4c688>

3D-SDF for #<Metabolite:0x00007fecfdb4c688>

PDB for #<Metabolite:0x00007fecfdb4c688>

3D PDB for #<Metabolite:0x00007fecfdb4c688>

SMILES for #<Metabolite:0x00007fecfdb4c688>

INCHI for #<Metabolite:0x00007fecfdb4c688>

Structure for #<Metabolite:0x00007fecfdb4c688>

3D Structure for #<Metabolite:0x00007fecfdb4c688>