MiMeDB: Showing metabocard for N1-(5-phospho-Œ≤-D-ribosyl)glycinamide (MMDBc0032166)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:05:10 UTC

Update Date

2022-08-31 18:31:05 UTC

Metabolite ID

MMDBc0032166

Metabolite Identification

Common Name

N1-(5-phospho-Œ≤-D-ribosyl)glycinamide

Description

N1-(5-phospho-beta-D-ribosyl)glycinamide is an intermediate in 5-aminoimidazole ribonucleotide biosynthesis I pathway in E.coli. It is a substrate for the enzyme phosphoribosylglycinamide formyltransferase 1 which catalyzes the reaction an N10-formyl-tetrahydrofolate + N1-(5-phospho-beta-D-ribosyl)glycinamide -> a tetrahydrofolate + N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + H+. It is also a product for enzyme phosphoribosylamine-glycine ligase which catalyzes reaction ATP + 5-phospho-beta-D-ribosylamine + glycine -> ADP + N1-(5-phospho-beta-D-ribosyl)glycinamide + phosphate + H+ (BioCYc: 5-PHOSPHO-RIBOSYL-GLYCINEAMIDE).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533005291517212D          

 18 18  0  0  0  0            999 V2000
   -0.2463    1.4371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2463    0.6121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4210    0.1272    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1661   -0.6574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6588   -0.6574    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9137    0.1272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1437   -1.3248    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8082   -2.0785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0122   -2.1647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2931   -2.7459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9575   -3.4996    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.6510   -1.3248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2057    0.3821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4681    1.8496    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4681    2.6746    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.4681    3.4996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2931    2.6746    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.3568    2.6746    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  2  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 12  1  0  0  0  0
  3 13  1  0  0  0  0
  1 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 15 18  1  0  0  0  0
M  CHG  3  11   1  17  -1  18  -1
M  END
> <DATABASE_ID>
MMDBc0032166

> <DATABASE_NAME>
MIME

> <SMILES>
[NH3+]CC(=O)NC1OC(COP([O-])([O-])=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-1

> <INCHI_KEY>
OBQMLSFOUZUIOB-UHFFFAOYSA-M

> <FORMULA>
C7H14N2O8P

> <MOLECULAR_WEIGHT>
285.169

> <EXACT_MASS>
285.049325997

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.91557353380736

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[5-(2-azaniumylacetamido)-3,4-dihydroxyoxolan-2-yl]methyl phosphate

> <ALOGPS_LOGP>
-1.90

> <JCHEM_LOGP>
-4.650616976017661

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.245768050847792

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255744528280514

> <JCHEM_PKA_STRONGEST_BASIC>
8.141960108603826

> <JCHEM_POLAR_SURFACE_AREA>
178.85000000000002

> <JCHEM_REFRACTIVITY>
64.3442

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.51e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(2-ammonioacetamido)-3,4-dihydroxyoxolan-2-yl]methyl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-MAY-15         0                                  
HETATM    1  C   UNK     0      -0.460   2.683   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.460   1.143   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.786   0.237   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.310  -1.227   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.230  -1.227   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.706   0.237   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -2.135  -2.473   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -1.509  -3.880   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.023  -4.041   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.414  -5.126   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -1.787  -6.533   0.000  0.00  0.00           N+1
HETATM   12  O   UNK     0       1.215  -2.473   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.251   0.713   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.874   3.453   0.000  0.00  0.00           O+0
HETATM   15  P   UNK     0       0.874   4.993   0.000  0.00  0.00           P+0
HETATM   16  O   UNK     0       0.874   6.533   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.414   4.993   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      -0.666   4.993   0.000  0.00  0.00           O-1
CONECT    1    2   14                                                       
CONECT    2    1    3    6                                                  
CONECT    3    2    4   13                                                  
CONECT    4    3    5   12                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    2                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10                                                            
CONECT   12    4                                                            
CONECT   13    3                                                            
CONECT   14    1   15                                                       
CONECT   15   14   16   17   18                                             
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   15                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Not Available

Molecular Formula

C₇H₁₄N₂O₈P

Average Mass

285.169

Monoisotopic Mass

285.049325997

IUPAC Name

[5-(2-azaniumylacetamido)-3,4-dihydroxyoxolan-2-yl]methyl phosphate

Traditional Name

[5-(2-ammonioacetamido)-3,4-dihydroxyoxolan-2-yl]methyl phosphate

CAS Registry Number

Not Available

SMILES

[NH3+]CC(=O)NC1OC(COP([O-])([O-])=O)C(O)C1O

InChI Identifier

InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-1

InChI Key

OBQMLSFOUZUIOB-UHFFFAOYSA-M

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

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	45.1 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-4.7	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	8.14	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	178.85 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	64.34 m³·mol⁻¹	ChemAxon
Polarizability	23.92 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 LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-9230000000-1055514d142206e7d587	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-9110000000-04d0f5553abcbd0fd252	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-003r-9200000000-9507b88a161e6ec8fdfa	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-3900000000-cf08513f99d80344c5f1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004r-9010000000-7f863cfb14b9195d2f64	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00fr-9000000000-ce632b84eee06368c6b2	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018506	Glycine	Hydrogen Ion	Phosphoribosylamine--glycine ligase	Ligation	PathBank	31602464
MMDBr0018507	Formic acid	Hydrogen Ion	Formate-dependent phosphoribosylglycinamide formyltransferase	Transfer of a formyl group	PathBank	31602464
MMDBr0019198	N1-(5-phospho-Œ≤-D-ribosyl)glycinamide	Hydrogen Ion	Phosphoribosylglycinamide formyltransferase	Transfer of a formyl group	PathBank	31602464
MMDBr0019836	Glycine	Hydrogen Ion	Not Available		PathBank	31602464
MMDBr0019837	Formic acid	Hydrogen Ion	Phosphoribosylaminoimidazole carboxylase	Carboxylation	PathBank	31602464

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25244572

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for N1-(5-phospho-Œ≤-D-ribosyl)glycinamide (MMDBc0032166)

MOL for #<Metabolite:0x0000564af381c6f0>

3D MOL for #<Metabolite:0x0000564af381c6f0>

3D SDF for #<Metabolite:0x0000564af381c6f0>

3D-SDF for #<Metabolite:0x0000564af381c6f0>

PDB for #<Metabolite:0x0000564af381c6f0>

3D PDB for #<Metabolite:0x0000564af381c6f0>

SMILES for #<Metabolite:0x0000564af381c6f0>

INCHI for #<Metabolite:0x0000564af381c6f0>

Structure for #<Metabolite:0x0000564af381c6f0>

3D Structure for #<Metabolite:0x0000564af381c6f0>