MiMeDB: Showing metabocard for (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate (MMDBc0031908)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:54:29 UTC

Update Date

2022-08-31 18:26:07 UTC

Metabolite ID

MMDBc0031908

Metabolite Identification

Common Name

(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate

Description

The dicarboxylic acid dianion formed from (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid by proton loss from both carboxy groups; major species present at pH 7.3

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1652303082006142D          

 13 13  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1433    1.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1433    2.0624    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.8578    0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  7  1  0  0  0  0
  5  8  1  0  0  0  0
  3 13  1  0  0  0  0
  7 12  2  0  0  0  0
  7 11  1  0  0  0  0
  8 10  1  0  0  0  0
  8  9  2  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
M  CHG  2  10  -1  11  -1
M  END
> <DATABASE_ID>
MMDBc0031908

> <DATABASE_NAME>
MIME

> <SMILES>
OC1CC(N=C(C1)C([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NO5/c9-3-1-4(6(10)11)8-5(2-3)7(12)13/h3-4,9H,1-2H2,(H,10,11)(H,12,13)/p-2

> <INCHI_KEY>
DVTPRYHENFBCII-UHFFFAOYSA-L

> <FORMULA>
C7H7NO5

> <MOLECULAR_WEIGHT>
185.136

> <EXACT_MASS>
185.033519489

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
15.633695079723172

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

> <ALOGPS_LOGP>
-0.90

> <JCHEM_LOGP>
-0.6398823156666666

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.866267430086415

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1319547579253704

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2648714552211295

> <JCHEM_POLAR_SURFACE_AREA>
112.85000000000001

> <JCHEM_REFRACTIVITY>
61.4158

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.04e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   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   1.540   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2    7    6                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    8    6                                                  
CONECT    6    5    1                                                       
CONECT    7    1   12   11                                                  
CONECT    8    5   10    9                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    3                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinic acid	Generator

Molecular Formula

C₇H₇NO₅

Average Mass

185.136

Monoisotopic Mass

185.033519489

IUPAC Name

4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

Traditional Name

4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate

CAS Registry Number

Not Available

SMILES

OC1CC(N=C(C1)C([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C7H9NO5/c9-3-1-4(6(10)11)8-5(2-3)7(12)13/h3-4,9H,1-2H2,(H,10,11)(H,12,13)/p-2

InChI Key

DVTPRYHENFBCII-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Tetrahydropyridine
Dicarboxylic acid or derivatives
Hydropyridine
Ketimine
Secondary alcohol
Carboxylic acid
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Imine
Organopnictogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	20.4 g/L	ALOGPS
logP	-0.9	ALOGPS
logP	-0.64	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	3.13	ChemAxon
pKa (Strongest Basic)	-2.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	112.85 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	61.42 m³·mol⁻¹	ChemAxon
Polarizability	15.63 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

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
MMDBr0015316	L-Aspartate-semialdehyde	(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate	4-hydroxy-tetrahydrodipicolinate synthase	Synthesis	RHEA	34755880
MMDBr0015402	(S)-2,3,4,5-tetrahydrodipicolinate	(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate	4-hydroxy-tetrahydrodipicolinate reductase	Reduction	RHEA	34755880
MMDBr0015405	(S)-2,3,4,5-tetrahydrodipicolinate	(2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate	4-hydroxy-tetrahydrodipicolinate reductase	Reduction	RHEA	34755880
MMDBr0018058	Pyruvic acid	Hydrogen Ion	4-hydroxy-tetrahydrodipicolinate synthase	Synthesis	PathBank	31602464
MMDBr0018059	Hydrogen Ion	NADP	4-hydroxy-tetrahydrodipicolinate reductase	Reduction	PathBank	31602464

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	Proteobacteria	377	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Dog ; Lion ; Chicken ; American dog tick ; River trout ; Human sputum; Human subgingival plaque	Unknown
Bacteria	Cyanobacteria	33	Human
Bacteria	Firmicutes	119	Human feces; Human ; Catfish ; Cattle
Bacteria	Tenericutes	1
Bacteria	Actinobacteria	40	Human ; Human feces; Cattle
Bacteria	Acidobacteria	2
Bacteria	Aquificae	4
Archaea/Archaea	Euryarchaeota	22
Bacteria	Bacteroidetes	10	Human ; Human feces
Bacteria	Spirochaetes	7	Pig ; Human
Bacteria	Chlamydiae	8	Human ; Sheep ; Cat
Bacteria	Chlorobi	11
Bacteria	Chloroflexi	4
Bacteria	Elusimicrobia	1
Bacteria	Thermotogae	8
Archaea	Euryarchaeota	2
Bacteria	nah	2
Bacteria	Deinococcus-thermus	2
Bacteria	Nitrospirae	1
Bacteria	Verrucomicrobia	1	Human ; Human feces
Bacteria	Dictyoglomi	2
Bacteria	Planctomycetes	1
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; Rat ; Sheep ; Dog ; Lion ; Chicken ; American dog tick ; River trout ; Human sputum; Human subgingival plaque	Unknown

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

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

77908689

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 (2S,4S)-4-Hydroxy-2,3,4,5-tetrahydrodipicolinate (MMDBc0031908)

MOL for #<Metabolite:0x00007f5abe013f40>

3D MOL for #<Metabolite:0x00007f5abe013f40>

3D SDF for #<Metabolite:0x00007f5abe013f40>

3D-SDF for #<Metabolite:0x00007f5abe013f40>

PDB for #<Metabolite:0x00007f5abe013f40>

3D PDB for #<Metabolite:0x00007f5abe013f40>

SMILES for #<Metabolite:0x00007f5abe013f40>

INCHI for #<Metabolite:0x00007f5abe013f40>

Structure for #<Metabolite:0x00007f5abe013f40>

3D Structure for #<Metabolite:0x00007f5abe013f40>