MiMeDB: Showing metabocard for 3-Hydroxysuberic acid (MMDBc0031984)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:57:32 UTC

Update Date

2024-04-30 19:53:56 UTC

Metabolite ID

MMDBc0031984

Metabolite Identification

Common Name

3-Hydroxysuberic acid

Description

NULL

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxysuberic acid.mol                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      -4.668  -0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.334   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.334  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.668   0.385   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.668  -1.925   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      -6.002   0.385   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.668   1.925   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.002  -0.385   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.001  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    9   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   13                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7   11   12                                                  
CONECT    9    1                                                            
CONECT   10    1                                                            
CONECT   11    8                                                            
CONECT   12    8                                                            
CONECT   13    3                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

COMPND    HMDB0000325
HETATM    1  O1  UNL     1      -5.053  -0.853  -0.159  1.00  0.00           O  
HETATM    2  C1  UNL     1      -4.071  -0.091   0.135  1.00  0.00           C  
HETATM    3  O2  UNL     1      -4.405   1.070   0.817  1.00  0.00           O  
HETATM    4  C2  UNL     1      -2.672  -0.441  -0.236  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.786   0.659   0.257  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.324   0.435  -0.053  1.00  0.00           C  
HETATM    7  C5  UNL     1       0.215  -0.812   0.553  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.669  -0.964   0.185  1.00  0.00           C  
HETATM    9  O3  UNL     1       1.842  -1.032  -1.200  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.463   0.140   0.789  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.929   0.015   0.444  1.00  0.00           C  
HETATM   12  O4  UNL     1       4.345  -0.926  -0.265  1.00  0.00           O  
HETATM   13  O5  UNL     1       4.752   1.010   0.970  1.00  0.00           O  
HETATM   14  H1  UNL     1      -4.187   2.000   0.491  1.00  0.00           H  
HETATM   15  H2  UNL     1      -2.641  -0.407  -1.358  1.00  0.00           H  
HETATM   16  H3  UNL     1      -2.388  -1.440   0.129  1.00  0.00           H  
HETATM   17  H4  UNL     1      -1.879   0.715   1.354  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.086   1.600  -0.226  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.076   0.486  -1.112  1.00  0.00           H  
HETATM   20  H7  UNL     1       0.195   1.310   0.439  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.142  -0.805   1.674  1.00  0.00           H  
HETATM   22  H9  UNL     1      -0.371  -1.719   0.249  1.00  0.00           H  
HETATM   23  H10 UNL     1       2.091  -1.929   0.567  1.00  0.00           H  
HETATM   24  H11 UNL     1       0.987  -1.225  -1.678  1.00  0.00           H  
HETATM   25  H12 UNL     1       2.185   1.134   0.360  1.00  0.00           H  
HETATM   26  H13 UNL     1       2.410   0.103   1.889  1.00  0.00           H  
HETATM   27  H14 UNL     1       4.715   1.971   0.605  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8   21   22
CONECT    8    9   10   23
CONECT    9   24
CONECT   10   11   25   26
CONECT   11   12   12   13
CONECT   13   27
END

Synonyms

Value	Source
3-Hydroxysuberate	Generator
3-Hydroxyoctanedioate	HMDB
3-Hydroxyoctanedioic acid	HMDB
3-Hydroxy-suberate	HMDB

Molecular Formula

C₈H₁₄O₅

Average Mass

190.1938

Monoisotopic Mass

190.084123558

IUPAC Name

3-hydroxyoctanedioic acid

Traditional Name

3-hydroxysuberic acid

CAS Registry Number

Not Available

SMILES

OC(CCCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C8H14O5/c9-6(5-8(12)13)3-1-2-4-7(10)11/h6,9H,1-5H2,(H,10,11)(H,12,13)

InChI Key

ARJZZFJXSNJKGR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain hydroxy acids and derivatives. These are hydroxy acids with a 6 to 12 carbon atoms long side chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Medium-chain hydroxy acids and derivatives

Direct Parent

Medium-chain hydroxy acids and derivatives

Alternative Parents

Substituents

Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Dicarboxylic acid or derivatives
Fatty acyl
Fatty acid
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dicarboxylic acid (CHEBI:70766 )
3-hydroxy carboxylic acid (CHEBI:70766 )
Dicarboxylic acids (LMFA01170093 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.5 g/L	ALOGPS
logP	-0.17	ALOGPS
logP	0.15	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	3.94	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	43.46 m³·mol⁻¹	ChemAxon
Polarizability	19.14 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9600000000-8161524f0f04ddabd28f	2017-09-01	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00a9-9185000000-26b8219023a90b94803c	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-052r-0900000000-c8110c0a94d4b56b34cb	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-053r-9300000000-4f9255a9b03fdc58054e	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-00pi-9000000000-cc672b33ccef862ae95b	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 6V, Positive	splash10-004i-1900000000-a0b84d8dc173f05ecfd5	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 6V, Negative	splash10-004i-1900000000-8cf7ff12fa71e34040a6	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-05fr-0900000000-61e1c6b1517c58dc0795	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-076r-1900000000-ad988528de191a2d13dc	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0bvu-9300000000-60e11695eca6da026124	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0079-0900000000-991a42c3d23f65a31306	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00g1-0900000000-e1fb76486e14d8491dde	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-9500000000-9846767c99c61860ada3	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00g0-0900000000-a3fda362228faa530ae1	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-3900000000-c74f29ced60b12eaaa94	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-14e61d30d5ca51ba50b7	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001r-5900000000-39bf66242dafebd87829	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-05fr-9200000000-b4ff1b0586d3b7059d94	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-6433a1c93128c79da322	2021-09-25	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Urine

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
MMDBr0008637	3-Hydoxy-Suberyl Coenzyme A	3-Hydroxysuberic acid	Not Available		VMH	30371894

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human Urine	Detected and Quantified	0.1			umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	2.7			umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	2.0	0.8	5.6	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	5.5	2.0	28.1	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	8087979
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Blood	Detected but not Quantified								HMDB

External Links

HMDB ID

HMDB0000325

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021951

KNApSAcK ID

Not Available

Chemspider ID

13498677

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5314

PubChem Compound

22328017

PDB ID

Not Available

ChEBI ID

70766

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Verhaeghe BJ, Van Bocxlaer JF, De Leenheer AP: Gas chromatographic/mass spectrometric identification of 3-hydroxydicarboxylic acids in urine. Biol Mass Spectrom. 1992 Jan;21(1):27-32. doi: 10.1002/bms.1200210107. [PubMed:1591279 ]
Tserng KY, Jin SJ: Metabolic origin of urinary 3-hydroxy dicarboxylic acids. Biochemistry. 1991 Mar 5;30(9):2508-14. doi: 10.1021/bi00223a030. [PubMed:2001377 ]
Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]

Showing metabocard for 3-Hydroxysuberic acid (MMDBc0031984)

MOL for #<Metabolite:0x00005634c2bd6418>

3D MOL for #<Metabolite:0x00005634c2bd6418>

3D SDF for #<Metabolite:0x00005634c2bd6418>

3D-SDF for #<Metabolite:0x00005634c2bd6418>

PDB for #<Metabolite:0x00005634c2bd6418>

3D PDB for #<Metabolite:0x00005634c2bd6418>

SMILES for #<Metabolite:0x00005634c2bd6418>

INCHI for #<Metabolite:0x00005634c2bd6418>

Structure for #<Metabolite:0x00005634c2bd6418>

3D Structure for #<Metabolite:0x00005634c2bd6418>