MiMeDB: Showing metabocard for XDP (MMDBc0030219)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:58:51 UTC

Update Date

2022-08-31 17:40:46 UTC

Metabolite ID

MMDBc0030219

Metabolite Identification

Common Name

XDP

Description

XDP is a member of the chemical class known as Purine Ribonucleoside Monophosphates. These are nucleotides consisting of a purine base linked to a ribose to which one monophosphate group is attached. . XDP is produced by the action of xanthosine triphosphatase when using XTP as a substrate.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05311207142D          

 32 34  0  0  0  0            999 V2000
   -1.8505   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9267   -7.1462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -6.4119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1924   -6.2394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9166   -4.3528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9468   -5.6877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0991   -5.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0129   -6.3257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4317   -5.0203    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7831   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7471   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4610   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4164   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  1  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
  9  6  1  0  0  0  0
 11  2  2  0  0  0  0
 11  4  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  2  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  7  1  0  0  0  0
  9 14  1  1  0  0  0
  5 15  1  6  0  0  0
  6 16  1  6  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  1  1  0  0  0  0
 25  3  1  0  0  0  0
 25  9  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  5 30  1  1  0  0  0
  6 31  1  1  0  0  0
  9 32  1  6  0  0  0
M  END


  Mrv0541 05311207142D          

 32 34  0  0  0  0            999 V2000
   -1.8505   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -3.2299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -3.4849    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0865   -2.8174    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -2.1500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -4.2695    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115   -2.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845   -1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9267   -7.1462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8334   -6.4119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1924   -6.2394    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9166   -4.3528    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9468   -5.6877    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7643   -4.5353    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831   -2.4049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0991   -5.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0129   -6.3257    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4317   -5.0203    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7831   -3.9515    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7471   -4.2326    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4610   -3.5525    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4164   -2.0209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  1  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  4  2  0  0  0  0
  8  4  1  0  0  0  0
  9  6  1  0  0  0  0
 11  2  2  0  0  0  0
 11  4  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  2  0  0  0  0
 13 10  1  0  0  0  0
 14  2  1  0  0  0  0
 14  7  1  0  0  0  0
  9 14  1  1  0  0  0
  5 15  1  6  0  0  0
  6 16  1  6  0  0  0
 17  8  1  0  0  0  0
 18 10  1  0  0  0  0
 24  1  1  0  0  0  0
 25  3  1  0  0  0  0
 25  9  1  0  0  0  0
 27 19  1  0  0  0  0
 27 20  1  0  0  0  0
 27 21  2  0  0  0  0
 27 26  1  0  0  0  0
 28 22  1  0  0  0  0
 28 23  2  0  0  0  0
 28 24  1  0  0  0  0
 28 26  1  0  0  0  0
  3 29  1  6  0  0  0
  5 30  1  1  0  0  0
  6 31  1  1  0  0  0
  9 32  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030219

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(=O)OP(O)(O)=O)O[C@@]([H])(N2C=NC3=C2N=C(O)N=C3O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H14N4O12P2/c15-5-3(1-24-28(22,23)26-27(19,20)21)25-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,22,23)(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1

> <INCHI_KEY>
YMOPVQQBWLGDOD-UUOKFMHZSA-N

> <FORMULA>
C10H14N4O12P2

> <MOLECULAR_WEIGHT>
444.1853

> <EXACT_MASS>
444.008344956

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
35.0704409430669

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,4R,5R)-5-(2,6-dihydroxy-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-0.98

> <JCHEM_LOGP>
-3.0698234138828098

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1395306132529996

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7801235740823467

> <JCHEM_PKA_STRONGEST_BASIC>
0.06920767325069843

> <JCHEM_POLAR_SURFACE_AREA>
247.03999999999994

> <JCHEM_REFRACTIVITY>
84.14879999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.73e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
XDP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-MAY-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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   28  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   29  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3   24                                                       
CONECT    2   11   14                                                       
CONECT    3    1    5   25   29                                             
CONECT    4    7    8   11                                                  
CONECT    5    3    6   15   30                                             
CONECT    6    5    9   16   31                                             
CONECT    7    4   12   14                                                  
CONECT    8    4   13   17                                                  
CONECT    9    6   14   25   32                                             
CONECT   10   12   13   18                                                  
CONECT   11    2    4                                                       
CONECT   12    7   10                                                       
CONECT   13    8   10                                                       
CONECT   14    2    7    9                                                  
CONECT   15    5                                                            
CONECT   16    6                                                            
CONECT   17    8                                                            
CONECT   18   10                                                            
CONECT   19   27                                                            
CONECT   20   27                                                            
CONECT   21   27                                                            
CONECT   22   28                                                            
CONECT   23   28                                                            
CONECT   24    1   28                                                       
CONECT   25    3    9                                                       
CONECT   26   27   28                                                       
CONECT   27   19   20   21   26                                             
CONECT   28   22   23   24   26                                             
CONECT   29    3                                                            
CONECT   30    5                                                            
CONECT   31    6                                                            
CONECT   32    9                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

Synonyms

Value	Source
Xanthosine 5'-pyrophosphate	Kegg
Xanthosine 5'-pyrophosphoric acid	Generator

Molecular Formula

C₁₀H₁₄N₄O₁₂P₂

Average Mass

444.1853

Monoisotopic Mass

444.008344956

IUPAC Name

[({[(2R,3S,4R,5R)-5-(2,6-dihydroxy-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

XDP

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(=O)OP(O)(O)=O)O[C@@]([H])(N2C=NC3=C2N=C(O)N=C3O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H14N4O12P2/c15-5-3(1-24-28(22,23)26-27(19,20)21)25-9(6(5)16)14-2-11-4-7(14)12-10(18)13-8(4)17/h2-3,5-6,9,15-16H,1H2,(H,22,23)(H2,19,20,21)(H2,12,13,17,18)/t3-,5-,6-,9-/m1/s1

InChI Key

YMOPVQQBWLGDOD-UUOKFMHZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose-5-phosphate
Pentose phosphate
Xanthine
Glycosyl compound
N-glycosyl compound
Purinone
6-oxopurine
Monosaccharide phosphate
Pentose monosaccharide
Organic pyrophosphate
Purine
Alkaloid or derivatives
Imidazopyrimidine
Monoalkyl phosphate
Pyrimidone
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Pyrimidine
Tetrahydrofuran
Heteroaromatic compound
Azole
Vinylogous amide
Imidazole
Secondary alcohol
Urea
1,2-diol
Lactam
Organoheterocyclic compound
Azacycle
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Alcohol
Organonitrogen compound
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

purine ribonucleoside 5'-diphosphate (CHEBI:10048 )
xanthosine 5'-phosphate (CHEBI:10048 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.73 g/L	ALOGPS
logP	-0.98	ALOGPS
logP	-3.1	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	0.069	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	247.04 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	84.15 m³·mol⁻¹	ChemAxon
Polarizability	35.07 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_6_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0911300000-8fb197d051b8b047ab95	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-fde58c7bd184206f70de	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udr-1900000000-a40a3e18996274054d7d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-1904600000-66f3ef8bf4ace2f9b713	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fbc-9700000000-6900e70120c26f5bcbe3	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9200000000-6f88e4eb1cb5282ba151	2015-09-15	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-17	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
MMDBr0014829	Water	Hydrogen Ion	Bifunctional phosphopantetheine adenylyltransferase/NTP phosphatase	Dephosphorylation	RHEA	34755880
MMDBr0019180	Xanthosine 5-triphosphate	Hydrogen Ion	Inosine/xanthosine triphosphatase	Dephosphorylation	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	61	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Archaea/Archaea	Euryarchaeota	8
Archaea/Archaea	Crenarchaeota	14
Bacteria	Firmicutes	2	Human feces
Archaea/Archaea	Korarchaeota	1
Archaea	Crenarchaeota	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

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

C01337

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

XDP

METLIN ID

Not Available

PubChem Compound

439486

PDB ID

Not Available

ChEBI ID

10048

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 ]
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 XDP (MMDBc0030219)

MOL for #<Metabolite:0x00007fa4e86c2318>

3D MOL for #<Metabolite:0x00007fa4e86c2318>

3D SDF for #<Metabolite:0x00007fa4e86c2318>

3D-SDF for #<Metabolite:0x00007fa4e86c2318>

PDB for #<Metabolite:0x00007fa4e86c2318>

3D PDB for #<Metabolite:0x00007fa4e86c2318>

SMILES for #<Metabolite:0x00007fa4e86c2318>

INCHI for #<Metabolite:0x00007fa4e86c2318>

Structure for #<Metabolite:0x00007fa4e86c2318>

3D Structure for #<Metabolite:0x00007fa4e86c2318>