MiMeDB: Showing metabocard for alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate (MMDBc0031928)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:55:20 UTC

Update Date

2022-08-31 18:26:31 UTC

Metabolite ID

MMDBc0031928

Metabolite Identification

Common Name

alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate

Description

A ribose bisphosphate that is the cyclic-1,2-phosphate derivative of 5-phospho-Œ±-D-ribose

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041521132D          
 
 17 18  0  0  1  0            999 V2000
   13.5056   -9.3121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8653   -9.6426    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.1874   -9.1349    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6082  -10.3866    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.5267   -9.6078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.7840  -10.3866    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.7409   -9.3540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1255   -9.9103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2911   -9.9103    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4601   -9.9103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2876  -10.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2876   -9.0792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6546  -11.2241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0781  -10.3021    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   14.9099   -9.7221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3361  -10.9747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.3031  -11.0517    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
  5  6  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  1 14  1  0  0  0  0
  4 16  1  6  0  0  0
  6 17  1  6  0  0  0
 16 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031928

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1[C@@H](COP(O)(O)=O)O[C@@H]2OP(O)(=O)O[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O10P2/c6-3-2(1-12-16(7,8)9)13-5-4(3)14-17(10,11)15-5/h2-6H,1H2,(H,10,11)(H2,7,8,9)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
OXGUIUWFXGIWNM-TXICZTDVSA-N

> <FORMULA>
C5H10O10P2

> <MOLECULAR_WEIGHT>
292.073

> <EXACT_MASS>
291.974920518

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.278615144831434

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-1.6527985473333333

> <ALOGPS_LOGS>
-1.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
1.691496559433233

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0421745627044876

> <JCHEM_PKA_STRONGEST_BASIC>
-3.702127883947399

> <JCHEM_POLAR_SURFACE_AREA>
151.98

> <JCHEM_REFRACTIVITY>
47.9277

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.06e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  O   UNK     0      25.210 -17.383   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      24.015 -18.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      22.750 -17.052   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      23.535 -19.388   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.517 -17.935   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      21.997 -19.388   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.050 -17.461   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      18.901 -18.499   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      17.343 -18.499   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      15.792 -18.499   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.337 -20.050   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      17.337 -16.948   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      27.355 -20.952   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0      26.279 -19.231   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      27.832 -18.148   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      24.894 -20.486   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      21.099 -20.630   0.000  0.00  0.00           O+0
CONECT    1    2   14                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2    6   16                                                  
CONECT    5    3    7    6                                                  
CONECT    6    4    5   17                                                  
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   14                                                            
CONECT   14   13   15    1   16                                             
CONECT   15   14                                                            
CONECT   16    4   14                                                       
CONECT   17    6                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

Synonyms

Value	Source
5-O-Phosphono-alpha-D-ribofuranose 1,2-(hydrogen phosphate)	ChEBI
PRCP	ChEBI
5-Phospho-alpha-D-ribose 1,2-cyclic phosphate	Kegg
5-O-Phosphono-a-D-ribofuranose 1,2-(hydrogen phosphate)	Generator
5-O-Phosphono-a-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-O-Phosphono-alpha-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-O-Phosphono-α-D-ribofuranose 1,2-(hydrogen phosphate)	Generator
5-O-Phosphono-α-D-ribofuranose 1,2-(hydrogen phosphoric acid)	Generator
5-Phospho-a-D-ribose 1,2-cyclic phosphate	Generator
5-Phospho-a-D-ribose 1,2-cyclic phosphoric acid	Generator
5-Phospho-alpha-D-ribose 1,2-cyclic phosphoric acid	Generator
5-Phospho-α-D-ribose 1,2-cyclic phosphate	Generator
5-Phospho-α-D-ribose 1,2-cyclic phosphoric acid	Generator
a-D-Ribose 1,2-cyclic phosphate 5-phosphate	Generator
a-D-Ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator
alpha-D-Ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator
Α-D-ribose 1,2-cyclic phosphate 5-phosphate	Generator
Α-D-ribose 1,2-cyclic phosphoric acid 5-phosphoric acid	Generator

Molecular Formula

C₅H₁₀O₁₀P₂

Average Mass

292.073

Monoisotopic Mass

291.974920518

IUPAC Name

{[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2H-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy}phosphonic acid

Traditional Name

[(3aR,5R,6R,6aR)-2,6-dihydroxy-2-oxo-tetrahydro-2λ⁵-furo[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COP(O)(O)=O)O[C@@H]2OP(O)(=O)O[C@H]12

InChI Identifier

InChI=1S/C5H10O10P2/c6-3-2(1-12-16(7,8)9)13-5-4(3)14-17(10,11)15-5/h2-6H,1H2,(H,10,11)(H2,7,8,9)/t2-,3-,4-,5-/m1/s1

InChI Key

OXGUIUWFXGIWNM-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
Alkyl phosphate
Phosphoric acid ester
1,3_dioxaphospholane
Tetrahydrofuran
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxide
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

ribose bisphosphate (CHEBI:68689 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.6 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-1.7	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	1.04	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	151.98 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	47.93 m³·mol⁻¹	ChemAxon
Polarizability	21.28 Å³	ChemAxon
Number of Rings	2	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 (TMS_4_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0007-1690000000-d822c489f37b24ff2975	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-6950000000-ffcb5885e5ecb4a2905a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0005-9400000000-03837736df41b9fe2d72	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002f-6190000000-409357fcff55c5c65e9e	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-43b002ba2f4ac1d81b59	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-f05162e8bfcafc437f6e	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-23	690.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-23	630.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-23	51.8
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	225.5
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	371.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	393.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	470.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	1102.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	1149.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	237.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	496.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-23	249.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	13.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	709.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	1119.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-23	135.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	513.7
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	711.5
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	669.9

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_1	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]2OP(=O)(O)O[C@@H]21	standard non polar	2025-10-24	1514.22
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_2	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H]2OP(=O)(O)O[C@@H]2[C@@H]1O	standard non polar	2025-10-24	1902.94
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_3	C[Si](C)(C)OP1(=O)O[C@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]2O1	standard non polar	2025-10-24	2062.99
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@@H]2OP(=O)(O)O[C@@H]21	standard non polar	2025-10-24	2086.89
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard non polar	2025-10-24	2592.86
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_6	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H]2OP(=O)(O)O[C@@H]2[C@@H]1O)O[Si](C)(C)C	standard non polar	2025-10-24	1935.24
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_7	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]2[C@@H]1O	standard non polar	2025-10-24	1964.51
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_8	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]2OP(=O)(O)O[C@@H]21	standard non polar	2025-10-24	1518.49
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard non polar	2025-10-24	2089.71
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_10	C[Si](C)(C)OP1(=O)O[C@H]2O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]2O1	standard non polar	2025-10-24	2341.83
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_11	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard non polar	2025-10-24	1716.53
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_1	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]2OP(=O)(O)O[C@@H]21	standard polar	2025-10-24	2581.91
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_2	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H]2OP(=O)(O)O[C@@H]2[C@@H]1O	standard polar	2025-10-24	1769.53
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_3	C[Si](C)(C)OP1(=O)O[C@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]2O1	standard polar	2025-10-24	2191.92
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_4	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@@H]2OP(=O)(O)O[C@@H]21	standard polar	2025-10-24	2771.54
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_5	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard polar	2025-10-24	1778.77
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_6	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H]2OP(=O)(O)O[C@@H]2[C@@H]1O)O[Si](C)(C)C	standard polar	2025-10-24	1974.64
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_7	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]2[C@@H]1O	standard polar	2025-10-24	2123.4
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_8	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]2OP(=O)(O)O[C@@H]21	standard polar	2025-10-24	1876.48
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O)O[Si](C)(C)C)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard polar	2025-10-24	1784.63
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_10	C[Si](C)(C)OP1(=O)O[C@H]2O[C@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)[C@@H](O)[C@H]2O1	standard polar	2025-10-24	1388.51
Gas Chromatography	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate_TMS_11	C[Si](C)(C)O[C@@H]1[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]2OP(=O)(O[Si](C)(C)C)O[C@@H]21	standard polar	2025-10-24	2471.62

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

Microbial Pathways

Pathways

Name	SMPDB/PathBank	Species
Methylphosphonate Degradation I		Escherichia coli Pseudomonas aeruginosa Escherichia coli SMS-3-5 Escherichia coli UTI89 Escherichia coli 55989 Escherichia coli SE11 Pseudomonas aeruginosa PA7 Escherichia coli CFT073 Ochrobactrum anthropi Pseudomonas stutzeri Klebsiella pneumoniae Eggerthella lenta DSM 2243 Methylobacterium nodulans Ochrobactrum anthropi ATCC 49188 Ochrobactrum intermedium LMG 3301 Odoribacter splanchnicus DSM 20712 Pseudomonas mendocina Pseudomonas syringae Bradyrhizobium japonicum Mesorhizobium loti Sinorhizobium meliloti Acidiphilium cryptum Chromobacterium violaceum Citrobacter koseri Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Desulfovibrio piger Acidithiobacillus ferrooxidans Rhodopseudomonas palustris Roseobacter denitrificans Thiobacillus denitrificans Holdemania filiformis Enterobacter cancerogenus Achromobacter xylosoxidans Methylibium petroleiphilum Citrobacter youngae Agrobacterium tumefaciens Klebsiella variicola Odoribacter splanchnicus Achromobacter xylosoxidans A8 Agrobacterium tumefaciens str. C58 Bradyrhizobium japonicum USDA 110 Citrobacter koseri ATCC BAA-895 Enterobacter cloacae subsp. cloacae ATCC 13047 Escherichia coli APEC O1 Escherichia coli E24377A Escherichia coli O127:H6 str. E2348/69 Escherichia coli UMN026 Escherichia coli ED1a Escherichia coli IAI39 Klebsiella pneumoniae subsp. pneumoniae MGH 78578 Laribacter hongkongensis HLHK9 Mesorhizobium loti MAFF303099 Methylobacterium radiotolerans JCM 2831 Escherichia coli 042 Pseudomonas fluorescens SBW25 Rhizobium leguminosarum bv. viciae 3841 Rhizobium leguminosarum bv. trifolii WSM2304 Shigella sonnei Ss046 Shigella dysenteriae Sd197 Yersinia enterocolitica subsp. enterocolitica 8081 Yersinia pseudotuberculosis IP 31758 Bradyrhizobium elkanii Methylobacterium mesophilicum Methylobacterium mesophilicum SR1.6/6 Rhizobium etli Azorhizobium caulinodans Xanthobacter autotrophicus Laribacter hongkongensis Bilophila wadsworthia 3_1_6 Desulfovibrio piger ATCC 29098 Cedecea davisae Cedecea davisae DSM 4568 Citrobacter amalonaticus Citrobacter amalonaticus Y19 Citrobacter freundii Citrobacter youngae ATCC 29220 Enterobacter hormaechei Klebsiella aerogenes Trabulsiella guamensis Trabulsiella guamensis ATCC 49490 Hafnia alvei Hafnia alvei ATCC 51873 Serratia marcescens subsp. marcescens Db11 Yersinia enterocolitica Yersinia pestis Yersinia pseudotuberculosis Grimontia hollisae CIP 101886 Collinsella tanakaei YIT 12063 Bacillus firmus DS1 [Clostridium] hylemonae DSM 15053 [Ruminococcus] gnavus ATCC 29149 [Clostridium] innocuum 2959 Holdemania filiformis DSM 12042 Ralstonia eutropha H16 Clostridioides difficile 630 Alkaliphilus metalliredigens QYMF Clavibacter michiganensis subsp. michiganensis NCPPB 382 Frankia sp. EuI1c Mycobacterium vanbaalenii PYR-1 Oceanobacillus iheyensis HTE831 Bacillus tusciae DSM 2912 Klebsiella aerogenes KCTC 2190 Acidiphilium cryptum JF-5 Acidiphilium multivorum AIU301 Acidithiobacillus ferrooxidans ATCC 23270 Acidovorax ebreus TPSY Agrobacterium vitis S4 Agrobacterium radiobacter K84 Rhodoferax ferrireducens T118 Arcobacter nitrofigilis DSM 7299 Azorhizobium caulinodans ORS 571 Bradyrhizobium sp. ORS278 Bradyrhizobium sp. BTAi1 Brucella melitensis bv. 1 str. 16M Brucella abortus bv. 1 str. 9-941 Brucella ovis ATCC 25840 Brucella canis ATCC 23365 Brucella suis ATCC 23445 Brucella abortus S19 Brucella melitensis ATCC 23457 Brucella microti CCM 4915 Burkholderia mallei ATCC 23344 Burkholderia pseudomallei 1710b Burkholderia xenovorans LB400 Burkholderia mallei NCTC 10229 Burkholderia pseudomallei 1106a Burkholderia phymatum STM815 Burkholderia phytofirmans PsJN Chloroflexus aurantiacus J-10-fl Chloroflexus aggregans DSM 9485 Cronobacter turicensis z3032 Cupriavidus metallidurans CH34 Cupriavidus taiwanensis LMG 19424 Cupriavidus necator N-1 Cyanothece sp. PCC 8801 Desulfomicrobium baculatum DSM 4028 Dickeya dadantii Ech703 Dickeya zeae Ech1591 Dickeya dadantii Ech586 Dickeya dadantii 3937 Enterobacter sp. 638 Enterobacter cloacae SCF1 Erwinia billingiae Eb661 Gluconobacter oxydans 621H Granulibacter bethesdensis CGDNIH1 Jannaschia sp. CCS1 Klebsiella pneumoniae 342 Marinobacter aquaeolei VT8 Methylibium petroleiphilum PM1 Methylobacterium nodulans ORS 2060 Nostoc sp. PCC 7120 Chromobacterium violaceum ATCC 12472 Synechococcus sp. JA-2-3B'a(2-13) Rhodobacter capsulatus SB1003 Pantoea ananatis LMG 20103 Paracoccus denitrificans PD1222 Pectobacterium atrosepticum SCRI1043 Pectobacterium carotovorum subsp. carotovorum PC1 Pseudomonas syringae pv. tomato str. DC3000 Pseudomonas syringae pv. phaseolicola 1448A Pseudomonas syringae pv. syringae B728a Psychromonas ingrahamii 37 Rhizobium etli CFN 42 Rhizobium etli CIAT 652 Rhizobium leguminosarum bv. trifolii WSM1325 Rhodopseudomonas palustris CGA009 Rhodopseudomonas palustris HaA2 Rhodopseudomonas palustris BisB5 Rhodospirillum centenum SW Roseiflexus sp. RS-1 Roseobacter denitrificans OCh 114 Roseobacter litoralis Och 149 Ruegeria pomeroyi DSS-3 Ruegeria sp. TM1040 Shigella boydii Sb227 Shigella boydii CDC 3083-94 Sinorhizobium meliloti 1021 Sinorhizobium medicae WSM419 Thiobacillus denitrificans ATCC 25259 Verminephrobacter eiseniae EF01-2 Xanthobacter autotrophicus Py2 Zymomonas mobilis subsp. pomaceae ATCC 29192 Klebsiella michiganensis KCTC 1686 Chania multitudinisentens RB-25

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019291	alpha-D-Ribose 1-methylphosphonate 5-phosphate	Methane	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464
MMDBr0019292	alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate	Ribose 1,5-bisphosphate	Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	PathBank	31602464
MMDBr0024932	S-Adenosylmethionine	Methane	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal	Unknown
Bacteria/Eubacteria	Actinobacteria	1	Human ; Human feces

Exposure Sources

Other Exposures

Source Type	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

C20440

BioCyc ID

CPD0-2463

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14035690

PDB ID

Not Available

ChEBI ID

68689

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 ]
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 alpha-D-Ribose 1,2-cyclic phosphate 5-phosphate (MMDBc0031928)

MOL for #<Metabolite:0x00007f2e518d4ab0>

3D MOL for #<Metabolite:0x00007f2e518d4ab0>

3D SDF for #<Metabolite:0x00007f2e518d4ab0>

3D-SDF for #<Metabolite:0x00007f2e518d4ab0>

PDB for #<Metabolite:0x00007f2e518d4ab0>

3D PDB for #<Metabolite:0x00007f2e518d4ab0>

SMILES for #<Metabolite:0x00007f2e518d4ab0>

INCHI for #<Metabolite:0x00007f2e518d4ab0>

Structure for #<Metabolite:0x00007f2e518d4ab0>

3D Structure for #<Metabolite:0x00007f2e518d4ab0>