MiMeDB: Showing metabocard for (R)-4'-phosphopantetheine (MMDBc0055040)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:40:33 UTC

Update Date

2022-08-12 20:09:12 UTC

Metabolite ID

MMDBc0055040

Metabolite Identification

Common Name

(R)-4'-phosphopantetheine

Description

D-pantetheine 4'-phosphate(2-), also known as (R)-4'-phosphopantetheine, belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom. Based on a literature review very few articles have been published on D-pantetheine 4'-phosphate(2-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221402D          

 23 22  0  0  1  0            999 V2000
    2.0625    1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4750   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.9500    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1250    1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1250   -2.8579    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  8  3  1  0  0  0  0
 10  9  1  0  0  0  0
 11  1  1  0  0  0  0
 11  2  1  0  0  0  0
 11  7  1  0  0  0  0
 11  9  1  0  0  0  0
 12  5  1  4  0  0  0
 12  8  2  0  0  0  0
 13  4  1  4  0  0  0
 13 10  2  0  0  0  0
 14  8  1  0  0  0  0
  9 15  1  1  0  0  0
 16 10  1  0  0  0  0
 20  7  1  0  0  0  0
 21 17  1  0  0  0  0
 21 18  1  0  0  0  0
 21 19  2  0  0  0  0
 21 20  1  0  0  0  0
 22  6  1  0  0  0  0
  9 23  1  1  0  0  0
M  CHG  2  14  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0055040

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H23N2O7PS/c1-11(2,7-20-21(17,18)19)9(15)10(16)13-4-3-8(14)12-5-6-22/h9,15,22H,3-7H2,1-2H3,(H,12,14)(H,13,16)(H2,17,18,19)/p-2/t9-/m0/s1

> <INCHI_KEY>
JDMUPRLRUUMCTL-VIFPVBQESA-L

> <FORMULA>
C11H21N2O7PS

> <MOLECULAR_WEIGHT>
356.33

> <EXACT_MASS>
356.081806356

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
33.029877366935665

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)-N-{2-[(2-sulfanylethyl)-C-hydroxycarbonimidoyl]ethyl}butanecarboximidate

> <JCHEM_LOGP>
-3.005848361965714

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.4112668470959098

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6093017351233656

> <JCHEM_PKA_STRONGEST_BASIC>
6.368425126298894

> <JCHEM_POLAR_SURFACE_AREA>
157.82999999999998

> <JCHEM_REFRACTIVITY>
103.7218

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)-N-{2-[(2-sulfanylethyl)-C-hydroxycarbonimidoyl]ethyl}butanecarboximidate

> <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       3.850   2.874   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -0.206   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.930  -4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.390   1.334   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -4.620  -2.667   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  O   UNK     0      -2.310  -4.001   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       1.540   2.667   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0       9.240   2.667   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       7.700   4.207   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.700   1.127   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.160   2.667   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0       7.700   2.667   0.000  0.00  0.00           P+0
HETATM   22  S   UNK     0      -7.700  -5.335   0.000  0.00  0.00           S+0
HETATM   23  H   UNK     0       3.080   0.000   0.000  0.00  0.00           H+0
CONECT    1   11                                                            
CONECT    2   11                                                            
CONECT    3    4    8                                                       
CONECT    4    3   13                                                       
CONECT    5    6   12                                                       
CONECT    6    5   22                                                       
CONECT    7   11   20                                                       
CONECT    8    3   12   14                                                  
CONECT    9   10   11   15   23                                             
CONECT   10    9   13   16                                                  
CONECT   11    1    2    7    9                                             
CONECT   12    5    8                                                       
CONECT   13    4   10                                                       
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16   10                                                            
CONECT   17   21                                                            
CONECT   18   21                                                            
CONECT   19   21                                                            
CONECT   20    7   21                                                       
CONECT   21   17   18   19   20                                             
CONECT   22    6                                                            
CONECT   23    9                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   44    0
END

Synonyms

Value	Source
(R)-4'-Phosphopantetheine	ChEBI
D-Pantetheine 4'-phosphoric acid(2-)	Generator

Molecular Formula

C₁₁H₂₁N₂O₇PS

Average Mass

356.33

Monoisotopic Mass

356.081806356

IUPAC Name

(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)-N-{2-[(2-sulfanylethyl)-C-hydroxycarbonimidoyl]ethyl}butanecarboximidate

Traditional Name

(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)-N-{2-[(2-sulfanylethyl)-C-hydroxycarbonimidoyl]ethyl}butanecarboximidate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(C([O-])=NCCC([O-])=NCCS)C(C)(C)COP(O)(O)=O

InChI Identifier

InChI=1S/C11H23N2O7PS/c1-11(2,7-20-21(17,18)19)9(15)10(16)13-4-3-8(14)12-5-6-22/h9,15,22H,3-7H2,1-2H3,(H,12,14)(H,13,16)(H2,17,18,19)/p-2/t9-/m0/s1

InChI Key

JDMUPRLRUUMCTL-VIFPVBQESA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Fatty amide
Monosaccharide
N-acyl-amine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Fatty acyl
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Alkylthiol
Carbonyl group
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

pantetheine 4'-phosphate(2-) (CHEBI:61723 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3	ChemAxon
pKa (Strongest Acidic)	1.61	ChemAxon
pKa (Strongest Basic)	6.37	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	157.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	103.72 m³·mol⁻¹	ChemAxon
Polarizability	33.03 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

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013566	Hydrogen Ion	(R)-4'-phosphopantetheine	Coenzyme A biosynthesis bifunctional protein CoaBC	Decarboxylation	RHEA	34755880
MMDBr0013921	(R)-4'-phosphopantetheine	3'-dephospho-CoA	Phosphopantetheine adenylyltransferase	Dephosphorylation	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	Proteobacteria	346	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Human sputum; Human subgingival plaque; Chicken
Bacteria	Firmicutes	153	Human feces; Human ; Catfish ; Cattle
Bacteria	Spirochaetes	18	Human ; Relapsing fever tick ; Pig
Archaea/Archaea	Euryarchaeota	14
Bacteria	Actinobacteria	52	Cattle ; Human ; Human feces
Bacteria	nah	1
Bacteria	Cyanobacteria	33	Human
Bacteria	Aquificae	1
Bacteria	Bacteroidetes	10	Human ; Human feces
Bacteria	Chloroflexi	10
Bacteria	Chlorobi	9
Bacteria	Deinococcus-thermus	5
Bacteria/NULL	Proteobacteria	2	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Human sputum; Human subgingival plaque; Chicken
Bacteria	Dictyoglomi	2
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Thermotogae	8
Bacteria	Verrucomicrobia	2
Bacteria	Tenericutes	4	Goat ; Human
Archaea/Archaea	Crenarchaeota	1
Bacteria	Planctomycetes	1
Bacteria	Nitrospirae	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

26332340

KEGG Compound ID

Not Available

BioCyc ID

PANTETHEINE-P

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25245905

PDB ID

Not Available

ChEBI ID

61723

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 (R)-4'-phosphopantetheine (MMDBc0055040)

MOL for #<Metabolite:0x00007f5a940215e8>

3D MOL for #<Metabolite:0x00007f5a940215e8>

3D SDF for #<Metabolite:0x00007f5a940215e8>

3D-SDF for #<Metabolite:0x00007f5a940215e8>

PDB for #<Metabolite:0x00007f5a940215e8>

3D PDB for #<Metabolite:0x00007f5a940215e8>

SMILES for #<Metabolite:0x00007f5a940215e8>

INCHI for #<Metabolite:0x00007f5a940215e8>

Structure for #<Metabolite:0x00007f5a940215e8>

3D Structure for #<Metabolite:0x00007f5a940215e8>