MiMeDB: Showing metabocard for 5'-phosphoribosyl-a-N-formylglycineamidine (MMDBc0032007)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:58:24 UTC

Update Date

2022-08-31 18:27:28 UTC

Metabolite ID

MMDBc0032007

Metabolite Identification

Common Name

5'-phosphoribosyl-a-N-formylglycineamidine

Description

NULL

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305171803382D          

 20 20  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2857   -0.7365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6212    0.0172    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7706   -1.4039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5911   -1.3177    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0760   -1.9851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6251    2.2012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0954    1.1616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5855    2.7308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8965   -1.8989    0.0000 O   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
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  2  0  0  0  0
 13  1  1  0  0  0  0
 11 20  1  4  0  0  0
M  END
> <DATABASE_ID>
MMDBc0032007

> <DATABASE_NAME>
MIME

> <SMILES>
OC=NCC(=N)NC1OC(COP(O)(O)=O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)

> <INCHI_KEY>
PMCOGCVKOAOZQM-UHFFFAOYSA-N

> <FORMULA>
C8H16N3O8P

> <MOLECULAR_WEIGHT>
313.2017

> <EXACT_MASS>
313.067501015

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.070332138691505

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({5-[(Z)-(1-amino-2-formamidoethylidene)amino]-3,4-dihydroxyoxolan-2-yl}methoxy)phosphonic acid

> <ALOGPS_LOGP>
-2.35

> <JCHEM_LOGP>
-4.1948904780062

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.993559096689065

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2239364580838377

> <JCHEM_PKA_STRONGEST_BASIC>
6.6007958599118535

> <JCHEM_POLAR_SURFACE_AREA>
183.92999999999995

> <JCHEM_REFRACTIVITY>
62.4273

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.58e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{5-[(Z)-(1-amino-2-formamidoethylidene)amino]-3,4-dihydroxyoxolan-2-yl}methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       2.735  -1.536   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.267  -1.375   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.893   0.032   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.172  -2.621   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       6.703  -2.460   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       7.609  -3.706   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.290  -0.290   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -3.436   3.633   0.000  0.00  0.00           P+0
HETATM   17  O   UNK     0      -4.900   4.109   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -3.911   2.168   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -2.960   5.098   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.140  -3.545   0.000  0.00  0.00           O+0
CONECT    1    2    3   13                                                  
CONECT    2    1                                                            
CONECT    3    1    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   20                                                       
CONECT   12    5   13                                                       
CONECT   13   12   14    1                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
CONECT   20   11                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

Synonyms

Not Available

Molecular Formula

C₈H₁₆N₃O₈P

Average Mass

313.2017

Monoisotopic Mass

313.067501015

IUPAC Name

({5-[(Z)-(1-amino-2-formamidoethylidene)amino]-3,4-dihydroxyoxolan-2-yl}methoxy)phosphonic acid

Traditional Name

{5-[(Z)-(1-amino-2-formamidoethylidene)amino]-3,4-dihydroxyoxolan-2-yl}methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OC=NCC(=N)NC1OC(COP(O)(O)=O)C(O)C1O

InChI Identifier

InChI=1S/C8H16N3O8P/c9-5(1-10-3-12)11-8-7(14)6(13)4(19-8)2-18-20(15,16)17/h3-4,6-8,13-14H,1-2H2,(H2,9,11)(H,10,12)(H2,15,16,17)

InChI Key

PMCOGCVKOAOZQM-UHFFFAOYSA-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
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid derivative
Alkyl phosphate
Phosphoric acid ester
Tetrahydrofuran
1,2-diol
Carboxamide group
Secondary carboxylic acid amide
Secondary alcohol
Amidine
Carboxylic acid amidine
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Alcohol
Organopnictogen compound
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	5.58 g/L	ALOGPS
logP	-2.4	ALOGPS
logP	-4.2	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	6.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.93 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	62.43 m³·mol⁻¹	ChemAxon
Polarizability	27.07 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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	splash10-01ot-7950000000-52597db3064d3890b1d7	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00lr-4953100000-00e5363247389e2ec22f	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-114i-8943000000-9f05701f1c7c206057be	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0kmi-9300000000-3257e95479d1c74ac02d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zmi-9400000000-3cf54beb907637f164a0	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0w4l-7913000000-78568b744ba16e38ce78	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9200000000-ac04e4a68ac6feb1d99f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-e307bc77b91245697f5b	2015-09-15	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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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

HMDB0062650

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022957

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

154

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 5'-phosphoribosyl-a-N-formylglycineamidine (MMDBc0032007)

MOL for #<Metabolite:0x00007f46bb63c550>

3D MOL for #<Metabolite:0x00007f46bb63c550>

3D SDF for #<Metabolite:0x00007f46bb63c550>

3D-SDF for #<Metabolite:0x00007f46bb63c550>

PDB for #<Metabolite:0x00007f46bb63c550>

3D PDB for #<Metabolite:0x00007f46bb63c550>

SMILES for #<Metabolite:0x00007f46bb63c550>

INCHI for #<Metabolite:0x00007f46bb63c550>

Structure for #<Metabolite:0x00007f46bb63c550>

3D Structure for #<Metabolite:0x00007f46bb63c550>