MiMeDB: Showing metabocard for aldehydo-D-ribose 5-phosphate (MMDBc0054326)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:07:07 UTC

Update Date

2022-09-01 02:28:29 UTC

Metabolite ID

MMDBc0054326

Metabolite Identification

Common Name

aldehydo-D-ribose 5-phosphate

Description

Ribose-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. The acyclic form of D-ribose 5-phosphate. Ribose-5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). In humans, ribose-5-phosphate is involved in pentose phosphate pathway.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 09041212592D          

 17 16  0  0  0  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8743    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599   -0.3020    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -1.1270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  2  0  0  0  0
  3  7  1  6  0  0  0
  4  8  1  6  0  0  0
  5  9  1  1  0  0  0
 13  2  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
  3 15  1  6  0  0  0
  4 16  1  6  0  0  0
  5 17  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054326

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1

> <INCHI_KEY>
PPQRONHOSHZGFQ-LMVFSUKVSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.748830472189866

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4R)-2,3,4-trihydroxy-5-oxopentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.64

> <JCHEM_LOGP>
-3.0615916523333335

> <ALOGPS_LOGS>
-1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.516819175661629

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4910102080971508

> <JCHEM_PKA_STRONGEST_BASIC>
-3.544450846242131

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.256

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-ribose 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4   13                                                       
CONECT    3    1    5    7   15                                             
CONECT    4    2    5    8   16                                             
CONECT    5    3    4    9   17                                             
CONECT    6    1                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12   14                                                            
CONECT   13    2   14                                                       
CONECT   14   10   11   12   13                                             
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    5                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

Synonyms

Value	Source
5-O-Phosphono-D-ribose	ChEBI
D-Ribose 5-phosphate	ChEBI
Ribose 5-phosphate	ChEBI
D-Ribose 5-phosphoric acid	Generator
Ribose 5-phosphoric acid	Generator
Ribose-5-phosphoric acid	Generator
Ribose-5-phosphoric acid, monobarium salt, (D-ribose)-isomer	MeSH
Ribose-5-phosphoric acid, (D-ribose)-isomer	MeSH
Ribose-5-phosphoric acid, (D-ribofuranose)-isomer	MeSH
D-Ribose-5-phosphoric acid	MeSH
Ribose phosphate	MeSH
Ribose 5-monophosphate	MeSH
Ribose-5-phosphoric acid, monosodium salt, (D-ribose)-isomer	MeSH
aldehydo-D-Ribose 5-phosphoric acid	Generator
Ribose-5-phosphate	MeSH

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.1098

Monoisotopic Mass

230.01915384

IUPAC Name

{[(2R,3R,4R)-2,3,4-trihydroxy-5-oxopentyl]oxy}phosphonic acid

Traditional Name

D-ribose 5-phosphate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h1,3-5,7-9H,2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1

InChI Key

PPQRONHOSHZGFQ-LMVFSUKVSA-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
Monosaccharide phosphate
Monoalkyl phosphate
Beta-hydroxy aldehyde
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Hydrocarbon derivative
Aldehyde
Organic oxide
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-ribose 5-phosphate (CHEBI:17797 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.3 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3.1	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.26 m³·mol⁻¹	ChemAxon
Polarizability	17.75 Å³	ChemAxon
Number of Rings	0	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
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-014i-1974000000-7f35421260bc9989530d	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (5 TMS)	splash10-014i-1975000000-858140fffa5338bc572e	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1932000000-ae42219f726995a7e3d5	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00kb-1932000000-48e9a0c4919c013906fb	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01ot-9610000000-071fe29dfef7d3466a18	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3690000000-fcd7107059f22c7a5f6b	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-638b56abde3ad27ae8d7	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-52548a47b2d250807082	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-a8ab09f348d154012f8f	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-853dc75e9fd92524e46f	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-66ec194b31d728583bb5	2017-07-26	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
MMDBr0012916	D-Glyceraldehyde 3-phosphate	aldehydo-D-ribose 5-phosphate	Transketolase	Transfer of ketol group	RHEA	34755880
MMDBr0012917	D-Glyceraldehyde 3-phosphate	aldehydo-D-ribose 5-phosphate	Transketolase 2	Transfer of ketol group	RHEA	34755880
MMDBr0012918	aldehydo-D-ribose 5-phosphate	D-Glyceraldehyde 3-phosphate	Transketolase 2	Transfer of ketol group	RHEA	34755880
MMDBr0013339	aldehydo-D-ribose 5-phosphate	D-Ribulose 5-phosphate	Bifunctional ribokinase/ribose-5-phosphate isomerase A	Isomerization	RHEA	34755880
MMDBr0017950	aldehydo-D-ribose 5-phosphate	Hydrogen Ion	Pyridoxal 5'-phosphate synthase subunit PDX1	Synthesis	RHEA	34755880

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
Bacteria	Firmicutes	136	Human feces; Human ; Cattle ; Catfish
Bacteria	Aquificae	1
Bacteria	Proteobacteria	283	Human ; Chicken ; Human feces; Pig ; Cattle ; River trout ; Turkey ; Sheep
Bacteria	Actinobacteria	56	Cattle ; Human ; Human feces
Bacteria	Tenericutes	2	Human
Bacteria	Cyanobacteria	25
Eukaryota/Fungi	Ascomycota	19	Human feces; Human saliva; Human supragingival plaque
Bacteria	Spirochaetes	7	Human
Archaea/Archaea	Euryarchaeota	36
Archaea/Archaea	Crenarchaeota	20
Bacteria	Chloroflexi	10
Bacteria	Chlamydiae	10	Human ; Sheep ; Cat
Eukaryota/Fungi	Basidiomycota	11	Human feces
Bacteria	Deinococcus-thermus	4
Bacteria/NULL	Proteobacteria	2	Human ; Chicken ; Human feces; Pig ; Cattle ; River trout ; Turkey ; Sheep
Archaea/Archaea	Korarchaeota	1
Bacteria	nah	1
Bacteria	Dictyoglomi	2
Bacteria	Fusobacteria	1	Human ; Human feces
Archaea	Euryarchaeota	3
Archaea	Crenarchaeota	1
Bacteria	Thermotogae	9
Bacteria	Bacteroidetes	1
Archaea/Archaea	Thaumarchaeota	2
Bacteria	Acidobacteria	2

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

DB02053

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

RIBOSE-5P

BiGG ID

Not Available

Wikipedia Link

D-ribose_5-phosphate

METLIN ID

Not Available

PubChem Compound

77982

PDB ID

Not Available

ChEBI ID

17797

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for aldehydo-D-ribose 5-phosphate (MMDBc0054326)

MOL for #<Metabolite:0x000055c79c3ae210>

3D MOL for #<Metabolite:0x000055c79c3ae210>

3D SDF for #<Metabolite:0x000055c79c3ae210>

3D-SDF for #<Metabolite:0x000055c79c3ae210>

PDB for #<Metabolite:0x000055c79c3ae210>

3D PDB for #<Metabolite:0x000055c79c3ae210>

SMILES for #<Metabolite:0x000055c79c3ae210>

INCHI for #<Metabolite:0x000055c79c3ae210>

Structure for #<Metabolite:0x000055c79c3ae210>

3D Structure for #<Metabolite:0x000055c79c3ae210>