NP-MRD: Showing NP-Card for Orotidylic acid (NP0333950)

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Record Information

Version

2.0

Created at

2024-09-09 21:23:52 UTC

Updated at

2024-09-09 21:23:52 UTC

NP-MRD ID

NP0333950

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Orotidylic acid

Description

Formed in the biosynthetic pathway in yeast Orotidine 5'-monophosphate (OMP), also known as orotidylic acid, is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate.; Orotidylic acid (OMP), is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate. Decarboxylation by Orotidylate decarboxylase affords Uridine 5'-phosphate which is the route to Uridine and its derivatives de novo and consequently one of the most important processes in nucleic acid synthesis (Dictionary of Organic Compounds). In humans, the enzyme UMP synthase converts OMP into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05242323562D          

 24 25  0  0  0  0            999 V2000
   -3.5251   -0.2280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3222    3.1152    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
   -1.3222    2.2902    0.0000 C   0  0  0  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
   -0.6548    1.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9097    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7347    1.0206    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3757    1.1931    0.0000 C   0  0  0  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
   -3.6744   -1.6491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1298    2.0602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4248    0.3532    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8908    1.8605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1962    1.2793    0.0000 O   0  0  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
   -0.6078    5.1777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2172    4.3527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4328    4.3527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    3.5277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9897    1.8053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078    4.3527    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  1  5  1  0  0  0  0
  2  4  1  0  0  0  0
  2 22  1  0  0  0  0
  3  9  1  0  0  0  0
  3 12  1  0  0  0  0
  4  6  1  0  0  0  0
  4 23  1  0  0  0  0
  5 11  2  0  0  0  0
  5 13  1  0  0  0  0
  6  7  1  0  0  0  0
  6 14  1  0  0  0  0
  7  8  1  0  0  0  0
  7 15  1  0  0  0  0
  8 12  1  0  0  0  0
  8 23  1  0  0  0  0
  9 16  2  0  0  0  0
  9 17  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 18  2  0  0  0  0
 19 24  1  0  0  0  0
 20 24  1  0  0  0  0
 21 24  2  0  0  0  0
 22 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0333950

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(COP(O)(O)=O)OC(C1O)N1C(=O)N=C(O)C=C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)

> <INCHI_KEY>
KYOBSHFOBAOFBF-UHFFFAOYNA-N

> <FORMULA>
C10H13N2O11P

> <MOLECULAR_WEIGHT>
368.191

> <EXACT_MASS>
368.025696245

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
29.48401554599367

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid

> <JCHEM_LOGP>
-2.543680869666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.2612506952985845

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.220351137019143

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6645684445537214

> <JCHEM_POLAR_SURFACE_AREA>
206.64999999999998

> <JCHEM_REFRACTIVITY>
71.0655

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-6-hydroxy-2-oxopyrimidine-4-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-MAY-23         0                                  
HETATM    1  C   UNK     0      -6.580  -0.426   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.468   5.815   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.675   0.820   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.468   4.275   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.954  -1.832   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.222   3.370   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.698   1.905   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.238   1.905   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.301   2.227   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      -6.859  -3.078   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.242   3.846   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.793   0.659   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -5.396   3.473   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -7.833   2.388   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.985  -0.909   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -1.134   9.665   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.406   8.125   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -2.674   8.125   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -1.134   6.585   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -3.714   3.370   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      -1.134   8.125   0.000  0.00  0.00           P+0
CONECT    1    3    5                                                       
CONECT    2    4   22                                                       
CONECT    3    1    9   12                                                  
CONECT    4    2    6   23                                                  
CONECT    5    1   11   13                                                  
CONECT    6    4    7   14                                                  
CONECT    7    6    8   15                                                  
CONECT    8    7   12   23                                                  
CONECT    9    3   16   17                                                  
CONECT   10   11   12   18                                                  
CONECT   11    5   10                                                       
CONECT   12    3    8   10                                                  
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    7                                                            
CONECT   16    9                                                            
CONECT   17    9                                                            
CONECT   18   10                                                            
CONECT   19   24                                                            
CONECT   20   24                                                            
CONECT   21   24                                                            
CONECT   22    2   24                                                       
CONECT   23    4    8                                                       
CONECT   24   19   20   21   22                                             
MASTER        0    0    0    0    0    0    0    0   24    0   50    0
END

View in JSmol

Synonyms

Value	Source
Orotidylate	Generator

Chemical Formula

C₁₀H₁₃N₂O₁₁P

Average Mass

368.1910 Da

Monoisotopic Mass

368.02570 Da

IUPAC Name

3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-6-hydroxy-2-oxo-2,3-dihydropyrimidine-4-carboxylic acid

Traditional Name

3-{3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl}-6-hydroxy-2-oxopyrimidine-4-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC1C(COP(O)(O)=O)OC(C1O)N1C(=O)N=C(O)C=C1C(O)=O

InChI Identifier

InChI=1/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)

InChI Key

KYOBSHFOBAOFBF-UHFFFAOYNA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound 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-5-phosphate
Pentose phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Pyrimidine-6-carboxylic acid or derivatives
Pyrimidine-6-carboxylic acid
Hydropyrimidine carboxylic acid derivative
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Pyrimidine
Alkyl phosphate
Phosphoric acid ester
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Urea
Lactam
1,2-diol
Organoheterocyclic compound
Carboxylic acid derivative
Carboxylic acid
Azacycle
Monocarboxylic acid or derivatives
Oxacycle
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organic nitrogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.5	ChemAxon
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	206.65 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	71.07 m³·mol⁻¹	ChemAxon
Polarizability	29.48 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Orotidine 5'-monophosphate

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Basharat Z, Ahmed I, Alnasser SM, Meshal A, Waheed Y: Exploring Lead-Like Molecules of Traditional Chinese Medicine for Treatment Quest against Aliarcobacter butzleri: In Silico Toxicity Assessment, Dynamics Simulation, and Pharmacokinetic Profiling. Biomed Res Int. 2024 Feb 22;2024:9377016. doi: 10.1155/2024/9377016. eCollection 2024. [PubMed:39282570 ]

Showing NP-Card for Orotidylic acid (NP0333950)

MOL for NP0333950 (Orotidylic acid)

3D MOL for NP0333950 (Orotidylic acid)

3D SDF for NP0333950 (Orotidylic acid)

3D-SDF for NP0333950 (Orotidylic acid)

PDB for NP0333950 (Orotidylic acid)

3D PDB for NP0333950 (Orotidylic acid)

SMILES for NP0333950 (Orotidylic acid)

INCHI for NP0333950 (Orotidylic acid)

Structure for NP0333950 (Orotidylic acid)

3D Structure for NP0333950 (Orotidylic acid)