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Showing metabocard for (S)-Methylmalonic acid semialdehyde (HMDB0002217)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-05-22 14:17:42 UTC
Update Date2021-09-14 15:20:03 UTC
HMDB IDHMDB0002217
Secondary Accession Numbers
  • HMDB02217
Metabolite Identification
Common Name(S)-Methylmalonic acid semialdehyde
Description(S)-Methylmalonic acid semialdehyde belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group (S)-Methylmalonic acid semialdehyde exists in all living organisms, ranging from bacteria to humans. In humans, (S)-methylmalonic acid semialdehyde is involved in the metabolic disorder called the 2-methyl-3-hydroxybutyryl-coa dehydrogenase deficiency pathway (S)-Methylmalonic acid semialdehyde has been detected, but not quantified in, several different foods, such as black-eyed peas (Vigna unguiculata ssp. unguiculata), vaccinium (blueberry, cranberry, huckleberry), leeks (Allium porrum), fenugreeks (Trigonella foenum-graecum), and sweet oranges (Citrus sinensis). This could make (S)-methylmalonic acid semialdehyde a potential biomarker for the consumption of these foods (S)-Methylmalonic acid semialdehyde is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a small amount of articles have been published on (S)-Methylmalonic acid semialdehyde.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

  Mrv1652306222023472D          

  8  7  0  0  1  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  6  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  3  8  1  1  0  0  0
M  END
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3D MOL for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

HMDB0002217
     RDKit          3D
(S)-Methylmalonic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.4143    0.1129    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0585    0.3244    0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5277    1.2924   -0.3872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.1152   -0.8055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8378   -0.9212    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075   -1.3197    1.4686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8046   -1.6009   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5913   -0.3013   -0.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -0.4875    1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8933    1.1194    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2104    0.7841    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556    1.2517   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -2.3696   -0.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  1
  3 12  1  0
  7 13  1  0
M  END
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3D SDF for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

  Mrv1652306222023472D          

  8  7  0  0  1  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  6  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  2  2  0  0  0  0
  6  4  2  0  0  0  0
  7  4  1  0  0  0  0
  3  8  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0002217

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@](C)(C=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1

> <INCHI_KEY>
VOKUMXABRRXHAR-VKHMYHEASA-N

> <FORMULA>
C4H6O3

> <MOLECULAR_WEIGHT>
102.0886

> <EXACT_MASS>
102.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
9.16242691245968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-methyl-3-oxopropanoic acid

> <ALOGPS_LOGP>
-0.00

> <JCHEM_LOGP>
0.05325275766666666

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
17.47521673394892

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9838439710362112

> <JCHEM_PKA_STRONGEST_BASIC>
-7.233962384073207

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
22.636900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-methylmalonaldehydic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

HMDB0002217
     RDKit          3D
(S)-Methylmalonic acid semialdehyde
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.4143    0.1129    0.4467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0585    0.3244    0.6514 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5277    1.2924   -0.3872 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2562    2.1152   -0.8055 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8378   -0.9212    0.4897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5075   -1.3197    1.4686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8046   -1.6009   -0.7227 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5913   -0.3013   -0.5528 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8087   -0.4875    1.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8933    1.1194    0.4733 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2104    0.7841    1.6464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5556    1.2517   -0.7550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4619   -2.3696   -0.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  2  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  1
  3 12  1  0
  7 13  1  0
M  END
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PDB for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

HEADER    PROTEIN                                 22-JUN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-JUN-20         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   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       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0       3.080   2.667   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    3    5                                                       
CONECT    3    1    2    4    8                                             
CONECT    4    3    6    7                                                  
CONECT    5    2                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

COMPND    HMDB0002217
HETATM    1  C1  UNL     1       1.414   0.113   0.447  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.058   0.324   0.651  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.528   1.292  -0.387  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.256   2.115  -0.806  1.00  0.00           O  
HETATM    5  C4  UNL     1      -0.838  -0.921   0.490  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.507  -1.320   1.469  1.00  0.00           O  
HETATM    7  O3  UNL     1      -0.805  -1.601  -0.723  1.00  0.00           O  
HETATM    8  H1  UNL     1       1.591  -0.301  -0.553  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.809  -0.488   1.271  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.893   1.119   0.473  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.210   0.784   1.646  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.556   1.252  -0.755  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.462  -2.370  -0.838  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    5   11
CONECT    3    4    4   12
CONECT    5    6    6    7
CONECT    7   13
END
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SMILES for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

[H][C@](C)(C=O)C(O)=O
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INCHI for HMDB0002217 ((S)-Methylmalonic acid semialdehyde)

InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(S)-Methylmalonate semialdehydeChEBI
(2S)-2-Methyl-3-oxopropanoateHMDB
(2S)-2-Methyl-3-oxopropanoic acidHMDB
Chemical FormulaC4H6O3
Average Molecular Weight102.0886
Monoisotopic Molecular Weight102.031694058
IUPAC Name(2S)-2-methyl-3-oxopropanoic acid
Traditional Name(S)-methylmalonaldehydic acid
CAS Registry Number99043-16-0
SMILES
C[C@@H](C=O)C(O)=O
InChI Identifier
InChI=1S/C4H6O3/c1-3(2-5)4(6)7/h2-3H,1H3,(H,6,7)/t3-/m0/s1
InChI KeyVOKUMXABRRXHAR-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 1,3-dicarbonyl compounds. These are carbonyl compounds with the generic formula O=C(R)C(H)C(R')=O, where R and R' can be any group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct Parent1,3-dicarbonyl compounds
Alternative Parents
Substituents
  • 1,3-dicarbonyl compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022912
KNApSAcK IDNot Available
Chemspider ID4575365
KEGG Compound IDC06002
BioCyc IDCH3-MALONATE-S-ALD
BiGG ID34698
Wikipedia LinkNot Available
METLIN ID6553
PubChem Compound5462303
PDB IDNot Available
ChEBI ID27821
Food Biomarker OntologyNot Available
VMH IDMMTSA
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Chambliss KL, Gray RG, Rylance G, Pollitt RJ, Gibson KM: Molecular characterization of methylmalonate semialdehyde dehydrogenase deficiency. J Inherit Metab Dis. 2000 Jul;23(5):497-504. [PubMed:10947204 ]
  2. Manning NJ, Pollitt RJ: Tracer studies of the interconversion of R- and S-methylmalonic semialdehydes in man. Biochem J. 1985 Oct 15;231(2):481-4. [PubMed:4062908 ]

Only showing the first 10 proteins. There are 14 proteins in total.

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Enzymes

Enzyme Details
1. Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Plays a role in valine and pyrimidine metabolism. Binds fatty acyl-CoA.
Gene Name:
ALDH6A1
Uniprot ID:
Q02252
Molecular weight:
57839.31
Reactions
(S)-Methylmalonic acid semialdehyde + Coenzyme A + NAD → Propionyl-CoA + Carbon dioxide + NADH + Hydrogen Iondetails
(S)-Methylmalonic acid semialdehyde + Coenzyme A + NAD → Methylmalonyl-CoA + NADH + Hydrogen Iondetails
Enzyme Details
2. Aldehyde oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
AOX1
Uniprot ID:
Q06278
Molecular weight:
147916.735
Reactions
Methylmalonic acid + Hydrogen peroxide → (S)-Methylmalonic acid semialdehyde + Oxygen + Waterdetails
Enzyme Details
3. 4-aminobutyrate aminotransferase, mitochondrial
General function:
Involved in 4-aminobutyrate transaminase activity
Specific function:
Catalyzes the conversion of gamma-aminobutyrate and L-beta-aminoisobutyrate to succinate semialdehyde and methylmalonate semialdehyde, respectively. Can also convert delta-aminovalerate and beta-alanine.
Gene Name:
ABAT
Uniprot ID:
P80404
Molecular weight:
56438.405
Reactions
(S)-beta-Aminoisobutyric acid + Oxoglutaric acid → (S)-Methylmalonic acid semialdehyde + Glutamic aciddetails
Enzyme Details
4. 4-trimethylaminobutyraldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Converts gamma-trimethylaminobutyraldehyde into gamma-butyrobetaine. Catalyzes the irreversible oxidation of a broad range of aldehydes to the corresponding acids in an NAD-dependent reaction.
Gene Name:
ALDH9A1
Uniprot ID:
P49189
Molecular weight:
56291.485
Reactions
(S)-Methylmalonic acid semialdehyde + NAD + Water → Methylmalonic acid + NADH + Hydrogen Iondetails
Enzyme Details
5. Alpha-aminoadipic semialdehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Multifunctional enzyme mediating important protective effects. Metabolizes betaine aldehyde to betaine, an important cellular osmolyte and methyl donor. Protects cells from oxidative stress by metabolizing a number of lipid peroxidation-derived aldehydes. Involved in lysine catabolism.
Gene Name:
ALDH7A1
Uniprot ID:
P49419
Molecular weight:
58486.74
Reactions
(S)-Methylmalonic acid semialdehyde + NAD + Water → Methylmalonic acid + NADH + Hydrogen Iondetails
Enzyme Details
6. Aldehyde dehydrogenase family 1 member A3
General function:
Involved in oxidoreductase activity
Specific function:
Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Seems to be the key enzyme in the formation of an RA gradient along the dorso-ventral axis during the early eye development and also in the development of the olfactory system (By similarity).
Gene Name:
ALDH1A3
Uniprot ID:
P47895
Molecular weight:
56107.995
Enzyme Details
7. Aldehyde dehydrogenase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
ALDH2
Uniprot ID:
P05091
Molecular weight:
56380.93
Reactions
(S)-Methylmalonic acid semialdehyde + NAD + Water → Methylmalonic acid + NADH + Hydrogen Iondetails
Enzyme Details
8. Fatty aldehyde dehydrogenase
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acids. Active on a variety of saturated and unsaturated aliphatic aldehydes between 6 and 24 carbons in length. Responsible for conversion of the sphingosine 1-phosphate (S1P) degradation product hexadecenal to hexadecenoic acid.
Gene Name:
ALDH3A2
Uniprot ID:
P51648
Molecular weight:
54847.36
Reactions
(S)-Methylmalonic acid semialdehyde + NAD + Water → Methylmalonic acid + NADH + Hydrogen Iondetails
Enzyme Details
9. Aldehyde dehydrogenase X, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
ALDHs play a major role in the detoxification of alcohol-derived acetaldehyde. They are involved in the metabolism of corticosteroids, biogenic amines, neurotransmitters, and lipid peroxidation.
Gene Name:
ALDH1B1
Uniprot ID:
P30837
Molecular weight:
57248.96
Reactions
(S)-Methylmalonic acid semialdehyde + NAD + Water → Methylmalonic acid + NADH + Hydrogen Iondetails
Enzyme Details
10. 3-hydroxyacyl-CoA dehydrogenase type-2
General function:
Involved in oxidoreductase activity
Specific function:
Functions in mitochondrial tRNA maturation. Part of mitochondrial ribonuclease P, an enzyme composed of MRPP1/TRMT10C, MRPP2/HSD17B10 and MRPP3/KIAA0391, which cleaves tRNA molecules in their 5'-ends. By interacting with intracellular amyloid-beta, it may contribute to the neuronal dysfunction associated with Alzheimer disease (AD).
Gene Name:
HSD17B10
Uniprot ID:
Q99714
Molecular weight:
25983.695

Only showing the first 10 proteins. There are 14 proteins in total.

Show all enzymes and transporters