MiMeDB: Showing metabocard for 5-methyl-UMP (MMDBc0055576)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:59:17 UTC

Update Date

2022-08-12 20:09:25 UTC

Metabolite ID

MMDBc0055576

Metabolite Identification

Common Name

5-methyl-UMP

Description

5-methyl-UMP belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. Based on a literature review very few articles have been published on 5-methyl-UMP.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221592D          

 26 27  0  0  1  0            999 V2000
   -4.3455   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3122    2.0180    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7825    0.9785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2726    2.5477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7429    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5257    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0573    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5730    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3602    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 11  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  2  1  0  0  0  0
  9 12  1  1  0  0  0
 12 10  1  0  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  8  1  0  0  0  0
 16 10  2  0  0  0  0
 20  3  1  0  0  0  0
 21  5  1  0  0  0  0
 21  9  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  5 23  1  6  0  0  0
  6 24  1  1  0  0  0
  7 25  1  1  0  0  0
  9 26  1  6  0  0  0
M  CHG  2  15  -1  17  -1
M  END


  Mrv1652306172221592D          

 26 27  0  0  1  0            999 V2000
   -4.3455   -0.1418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0401    0.4394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6548    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3222    2.2902    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1895   -0.9817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8841   -0.4005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3690   -1.0679    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2197    0.3532    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7743    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6744   -1.6491    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.0636   -0.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3122    2.0180    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7825    0.9785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2726    2.5477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7429    1.5082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5275    1.7631    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5257    2.6201    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0573    2.6647    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5730    1.2219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3602    0.2856    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  1  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 11  8  2  0  0  0  0
 11 10  1  0  0  0  0
 12  2  1  0  0  0  0
  9 12  1  1  0  0  0
 12 10  1  0  0  0  0
  6 13  1  6  0  0  0
  7 14  1  6  0  0  0
 15  8  1  0  0  0  0
 16 10  2  0  0  0  0
 20  3  1  0  0  0  0
 21  5  1  0  0  0  0
 21  9  1  0  0  0  0
 22 17  1  0  0  0  0
 22 18  1  0  0  0  0
 22 19  2  0  0  0  0
 22 20  1  0  0  0  0
  5 23  1  6  0  0  0
  6 24  1  1  0  0  0
  7 25  1  1  0  0  0
  9 26  1  6  0  0  0
M  CHG  2  15  -1  17  -1
M  END
> <DATABASE_ID>
MMDBc0055576

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)([O-])=O)O[C@@]([H])(N2C=C(C)C([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N2O9P/c1-4-2-12(10(16)11-8(4)15)9-7(14)6(13)5(21-9)3-20-22(17,18)19/h2,5-7,9,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/p-2/t5-,6-,7-,9-/m1/s1

> <INCHI_KEY>
IGWHDMPTQKSDTL-JXOAFFINSA-L

> <FORMULA>
C10H13N2O9P

> <MOLECULAR_WEIGHT>
336.194

> <EXACT_MASS>
336.036964164

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.74696319950568

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-5-methyl-2-oxo-1,2-dihydropyrimidin-4-olate

> <JCHEM_LOGP>
-1.775756879333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.228688853657535

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2255018350079596

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6645542177080603

> <JCHEM_POLAR_SURFACE_AREA>
175.00999999999996

> <JCHEM_REFRACTIVITY>
77.54589999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -8.112  -0.265   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.675   0.820   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.242   3.846   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.580  -0.426   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.714   3.370   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.954  -1.832   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.517  -0.748   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -4.422  -1.993   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0      -4.143   0.659   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -2.468   5.815   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -5.179   3.846   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -6.859  -3.078   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      -1.985  -0.909   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.316   3.767   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0       3.327   1.826   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.376   4.756   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.387   2.815   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -1.698   1.905   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       2.851   3.291   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0      -0.981   4.891   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -3.840   4.974   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -4.803   2.281   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.539   0.533   0.000  0.00  0.00           H+0
CONECT    1    4                                                            
CONECT    2    4   12                                                       
CONECT    3    5   20                                                       
CONECT    4    1    2    8                                                  
CONECT    5    3    6   21   23                                             
CONECT    6    5    7   13   24                                             
CONECT    7    6    9   14   25                                             
CONECT    8    4   11   15                                                  
CONECT    9    7   12   21   26                                             
CONECT   10   11   12   16                                                  
CONECT   11    8   10                                                       
CONECT   12    2    9   10                                                  
CONECT   13    6                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16   10                                                            
CONECT   17   22                                                            
CONECT   18   22                                                            
CONECT   19   22                                                            
CONECT   20    3   22                                                       
CONECT   21    5    9                                                       
CONECT   22   17   18   19   20                                             
CONECT   23    5                                                            
CONECT   24    6                                                            
CONECT   25    7                                                            
CONECT   26    9                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Not Available

Molecular Formula

C₁₀H₁₃N₂O₉P

Average Mass

336.194

Monoisotopic Mass

336.036964164

IUPAC Name

1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-5-methyl-2-oxo-1,2-dihydropyrimidin-4-olate

Traditional Name

1-[(2R,3R,4S,5R)-5-[(hydrogen phosphonooxy)methyl]-3,4-dihydroxyoxolan-2-yl]-5-methyl-2-oxopyrimidin-4-olate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)([O-])=O)O[C@@]([H])(N2C=C(C)C([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C10H15N2O9P/c1-4-2-12(10(16)11-8(4)15)9-7(14)6(13)5(21-9)3-20-22(17,18)19/h2,5-7,9,13-14H,3H2,1H3,(H,11,15,16)(H2,17,18,19)/p-2/t5-,6-,7-,9-/m1/s1

InChI Key

IGWHDMPTQKSDTL-JXOAFFINSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Vinylogous amide
Heteroaromatic compound
Oxolane
1,2-diol
Urea
Secondary alcohol
Lactam
Azacycle
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organic nitrogen compound
Alcohol
Organic oxide
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.8	ChemAxon
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	175.01 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	77.55 m³·mol⁻¹	ChemAxon
Polarizability	27.75 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

Not Available

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
Bacteria	Firmicutes	1	Human feces
Bacteria	Proteobacteria	1
Eukaryota/Fungi	Ascomycota	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

10463795

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

23421210

PDB ID

Not Available

ChEBI ID

Not Available

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 5-methyl-UMP (MMDBc0055576)

MOL for #<Metabolite:0x00005634c29dd260>

3D MOL for #<Metabolite:0x00005634c29dd260>

3D SDF for #<Metabolite:0x00005634c29dd260>

3D-SDF for #<Metabolite:0x00005634c29dd260>

PDB for #<Metabolite:0x00005634c29dd260>

3D PDB for #<Metabolite:0x00005634c29dd260>

SMILES for #<Metabolite:0x00005634c29dd260>

INCHI for #<Metabolite:0x00005634c29dd260>

Structure for #<Metabolite:0x00005634c29dd260>

3D Structure for #<Metabolite:0x00005634c29dd260>