MiMeDB: Showing metabocard for Succinate-semialdehyde-thiamine PPi (MMDBc0031710)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:45:19 UTC

Update Date

2022-08-31 18:23:41 UTC

Metabolite ID

MMDBc0031710

Metabolite Identification

Common Name

Succinate-semialdehyde-thiamine PPi

Description

Succinate-semialdehyde-thiamine pyrophosphate is a thiamine derivative. The first intermediate (SHCHC) in the menaquinone biosynthetic pathway, requires two reactions. The first is the decarboxylation of alpha-ketoglutarate by an alpha-ketoglutarate decarboxylase, which results in the formation of succinic semialdehyde-thiamine PPi (TPP) anion, and the second is the addition of the succinic semialdehyde-TPP anion to isochorismate, which is carried out by the enzyme SHCHC synthase. Both enzymatic activities are encoded by the menD gene [PMID: 1459959 ]

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 08141218132D          

 33 34  0  0  0  0            999 V2000
    0.5846   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8946    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8774   -9.6742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5418   -8.9205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1393   -3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4748   -3.9898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3925  -10.3417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0267   -8.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -1.2991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801   -0.0616    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -1.2991    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.7280  -11.0953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4280  -10.2554    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8472   -8.3393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5718   -5.7464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0792   -5.0753    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5087   -6.3471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8436   -7.3169    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.9899   -4.6572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6912   -7.4994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6610   -6.1646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3255   -5.4109    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.1761   -6.8320    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.5687    0.0000 S   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
 10  1  1  0  0  0  0
 11  2  1  0  0  0  0
 12  7  2  0  0  0  0
 12  8  1  0  0  0  0
 13  5  1  0  0  0  0
 13 10  2  0  0  0  0
 14  3  1  0  0  0  0
 15  4  1  0  0  0  0
 16 12  1  0  0  0  0
 17 16  2  0  0  0  0
 18  7  1  0  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
 19 16  1  0  0  0  0
 20  8  1  0  0  0  0
 20  9  2  0  0  0  0
 20 10  1  0  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23 15  1  0  0  0  0
 28  6  1  0  0  0  0
 29 15  1  0  0  0  0
 31 24  2  0  0  0  0
 31 25  1  0  0  0  0
 31 28  1  0  0  0  0
 31 30  1  0  0  0  0
 32 26  2  0  0  0  0
 32 27  1  0  0  0  0
 32 29  1  0  0  0  0
 32 30  1  0  0  0  0
 33  9  1  0  0  0  0
 33 13  1  0  0  0  0
M  CHG  4  20   1  22  -1  25  -1  27  -1
M  END


  Mrv0541 08141218132D          

 33 34  0  0  0  0            999 V2000
    0.5846   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8946    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8774   -9.6742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5418   -8.9205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1393   -3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4748   -3.9898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3925  -10.3417    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0267   -8.2531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656   -1.2991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1801   -0.0616    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -1.2991    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.7280  -11.0953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4280  -10.2554    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8472   -8.3393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5718   -5.7464    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0792   -5.0753    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.5087   -6.3471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8436   -7.3169    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.9899   -4.6572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6912   -7.4994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6610   -6.1646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3255   -5.4109    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.1761   -6.8320    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.4492   -2.5687    0.0000 S   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
 10  1  1  0  0  0  0
 11  2  1  0  0  0  0
 12  7  2  0  0  0  0
 12  8  1  0  0  0  0
 13  5  1  0  0  0  0
 13 10  2  0  0  0  0
 14  3  1  0  0  0  0
 15  4  1  0  0  0  0
 16 12  1  0  0  0  0
 17 16  2  0  0  0  0
 18  7  1  0  0  0  0
 18 11  2  0  0  0  0
 19 11  1  0  0  0  0
 19 16  1  0  0  0  0
 20  8  1  0  0  0  0
 20  9  2  0  0  0  0
 20 10  1  0  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23 15  1  0  0  0  0
 28  6  1  0  0  0  0
 29 15  1  0  0  0  0
 31 24  2  0  0  0  0
 31 25  1  0  0  0  0
 31 28  1  0  0  0  0
 31 30  1  0  0  0  0
 32 26  2  0  0  0  0
 32 27  1  0  0  0  0
 32 29  1  0  0  0  0
 32 30  1  0  0  0  0
 33  9  1  0  0  0  0
 33 13  1  0  0  0  0
M  CHG  4  20   1  22  -1  25  -1  27  -1
M  END
> <DATABASE_ID>
MMDBc0031710

> <DATABASE_NAME>
MIME

> <SMILES>
CC1=C(CCOP([O-])(=O)OP([O-])(=O)OC(O)CCC([O-])=O)SC=[N+]1CC1=CN=C(C)NC1=N

> <INCHI_IDENTIFIER>
InChI=1S/C16H24N4O10P2S/c1-10-13(33-9-20(10)8-12-7-18-11(2)19-16(12)17)5-6-28-31(24,25)30-32(26,27)29-15(23)4-3-14(21)22/h7,9,15,23H,3-6,8H2,1-2H3,(H4-,17,18,19,21,22,24,25,26,27)/p-2

> <INCHI_KEY>
JUWXHVVKSHTJQQ-UHFFFAOYSA-L

> <FORMULA>
C16H22N4O10P2S

> <MOLECULAR_WEIGHT>
524.379

> <EXACT_MASS>
524.053186658

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
45.627853514289185

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[2-({[(3-carboxylato-1-hydroxypropyl phosphonato)oxy]phosphinato}oxy)ethyl]-3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium

> <ALOGPS_LOGP>
-0.99

> <JCHEM_LOGP>
-8.256656570133059

> <ALOGPS_LOGS>
-3.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.726481708676381

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7192871596570996

> <JCHEM_PKA_STRONGEST_BASIC>
7.0359157204724845

> <JCHEM_POLAR_SURFACE_AREA>
220.42999999999998

> <JCHEM_REFRACTIVITY>
133.67779999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.51e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(2-{[(3-carboxylato-1-hydroxypropyl phosphonato)oxyphosphinato]oxy}ethyl)-3-[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 14-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-AUG-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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+1
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-1
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-1
HETATM   26  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   32  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   33  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
CONECT    1   10                                                            
CONECT    2   11                                                            
CONECT    3    4   14                                                       
CONECT    4    3   15                                                       
CONECT    5    6   13                                                       
CONECT    6    5   28                                                       
CONECT    7   12   18                                                       
CONECT    8   12   20                                                       
CONECT    9   20   33                                                       
CONECT   10    1   13   20                                                  
CONECT   11    2   18   19                                                  
CONECT   12    7    8   16                                                  
CONECT   13    5   10   33                                                  
CONECT   14    3   21   22                                                  
CONECT   15    4   23   29                                                  
CONECT   16   12   17   19                                                  
CONECT   17   16                                                            
CONECT   18    7   11                                                       
CONECT   19   11   16                                                       
CONECT   20    8    9   10                                                  
CONECT   21   14                                                            
CONECT   22   14                                                            
CONECT   23   15                                                            
CONECT   24   31                                                            
CONECT   25   31                                                            
CONECT   26   32                                                            
CONECT   27   32                                                            
CONECT   28    6   31                                                       
CONECT   29   15   32                                                       
CONECT   30   31   32                                                       
CONECT   31   24   25   28   30                                             
CONECT   32   26   27   29   30                                             
CONECT   33    9   13                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

Synonyms

Value	Source
Succinic acid-semialdehyde-thiamine ppi	Generator

Molecular Formula

C₁₆H₂₂N₄O₁₀P₂S

Average Mass

524.379

Monoisotopic Mass

524.053186658

IUPAC Name

5-[2-({[(3-carboxylato-1-hydroxypropyl phosphonato)oxy]phosphinato}oxy)ethyl]-3-[(6-imino-2-methyl-1,6-dihydropyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium

Traditional Name

5-(2-{[(3-carboxylato-1-hydroxypropyl phosphonato)oxyphosphinato]oxy}ethyl)-3-[(4-imino-2-methyl-3H-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium

CAS Registry Number

Not Available

SMILES

CC1=C(CCOP([O-])(=O)OP([O-])(=O)OC(O)CCC([O-])=O)SC=[N+]1CC1=CN=C(C)NC1=N

InChI Identifier

InChI=1S/C16H24N4O10P2S/c1-10-13(33-9-20(10)8-12-7-18-11(2)19-16(12)17)5-6-28-31(24,25)30-32(26,27)29-15(23)4-3-14(21)22/h7,9,15,23H,3-6,8H2,1-2H3,(H4-,17,18,19,21,22,24,25,26,27)/p-2

InChI Key

JUWXHVVKSHTJQQ-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as thiamine phosphates. These are thiamine derivatives in which the hydroxyl group of the ethanol moiety is substituted by a phosphate group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Thiamine phosphates

Alternative Parents

Substituents

Thiamine-phosphate
Organic pyrophosphate
4,5-disubstituted 1,3-thiazole
Imidolactam
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Hydropyrimidine
Heteroaromatic compound
Thiazole
Azole
Carboxylic acid salt
Azacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD0-2102 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.25 g/L	ALOGPS
logP	-0.99	ALOGPS
logP	-8.3	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	1.72	ChemAxon
pKa (Strongest Basic)	7.04	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	220.43 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	133.68 m³·mol⁻¹	ChemAxon
Polarizability	45.63 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

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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45479398

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]

Showing metabocard for Succinate-semialdehyde-thiamine PPi (MMDBc0031710)

MOL for #<Metabolite:0x00007f923cbb4880>

3D MOL for #<Metabolite:0x00007f923cbb4880>

3D SDF for #<Metabolite:0x00007f923cbb4880>

3D-SDF for #<Metabolite:0x00007f923cbb4880>

PDB for #<Metabolite:0x00007f923cbb4880>

3D PDB for #<Metabolite:0x00007f923cbb4880>

SMILES for #<Metabolite:0x00007f923cbb4880>

INCHI for #<Metabolite:0x00007f923cbb4880>

Structure for #<Metabolite:0x00007f923cbb4880>

3D Structure for #<Metabolite:0x00007f923cbb4880>