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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:49 UTC

Update Date

2023-02-21 17:18:09 UTC

HMDB ID

HMDB0014405

Secondary Accession Numbers

HMDB14405

Metabolite Identification

Common Name

Cycloserine

Description

Cycloserine is only found in individuals that have used or taken this drug. It is an antibiotic substance produced by Streptomyces garyphalus. [PubChem]Cycloserine is an analog of the amino acid D-alanine. It interferes with an early step in bacterial cell wall synthesis in the cytoplasm by competitive inhibition of two enzymes, L-alanine racemase, which forms D-alanine from L-alanine, and D-alanylalanine synthetase, which incorporates D-alanine into the pentapeptide necessary for peptidoglycan formation and bacterial cell wall synthesis.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(+)-4-Amino-3-isoxazolidinone	ChEBI
(+)-Cycloserine	ChEBI
(R)-4-AMINO-isoxazolidin-3-one	ChEBI
alpha-Cycloserine	ChEBI
Cicloserina	ChEBI
Cyclo-D-serine	ChEBI
Cycloserinum	ChEBI
D-(+)-Cycloserine	ChEBI
D-4-Amino-3-isoxazolidinone	ChEBI
D-4-Amino-3-isoxazolidone	ChEBI
DCS	ChEBI
Orientomycin	ChEBI
PA 94	ChEBI
PA-94	ChEBI
Ro-1-9213	ChEBI
Seromycin	ChEBI
D-Cycloserine	Kegg
ABBR DCS	Kegg
a-Cycloserine	Generator
Α-cycloserine	Generator
D-CS	HMDB
D-Cycloserine synth. BP 88	HMDB
D-Cycloserine, synthetic	HMDB
D-Oxamicina	HMDB
D-Oxamycin	HMDB
DL-Cycloserine	HMDB
L-Cycloserine	HMDB
R-4-Amino-3-isoxazolidinone	HMDB

Chemical Formula

C₃H₆N₂O₂

Average Molecular Weight

102.0919

Monoisotopic Molecular Weight

102.042927446

IUPAC Name

(4R)-4-amino-1,2-oxazolidin-3-one

Traditional Name

cycloserine

CAS Registry Number

68-41-7

SMILES

[H][C@@]1(N)CON=C1O

InChI Identifier

InChI=1S/C3H6N2O2/c4-2-1-7-5-3(2)6/h2H,1,4H2,(H,5,6)/t2-/m1/s1

InChI Key

DYDCUQKUCUHJBH-UWTATZPHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoxazolines. Isoxazolines are compounds containing a five-member unsaturated aliphatic ring, with an oxygen atom adjacent to a nitrogen atoms, and three carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azolines

Sub Class

Isoxazolines

Direct Parent

Isoxazolines

Alternative Parents

Substituents

Isoxazoline
Oxacycle
Azacycle
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

organooxygen heterocyclic antibiotic (CHEBI:40009 )
organonitrogen heterocyclic antibiotic (CHEBI:40009 )
4-amino-1,2-oxazolidin-3-one (CHEBI:40009 )
Non-ribosomal peptide/polyketide hybrids (C08057 )
Non-ribosomal peptide/polyketide hybrids (LMPK14000007 )

Ontology

Not Available

Not Available

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	147 °C	Not Available
Boiling Point	189.27 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	877 g/L	Not Available
LogP	-0.9	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	877 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-2.4	ChemAxon
logS	-0.15	ALOGPS
pKa (Strongest Acidic)	4.21	ChemAxon
pKa (Strongest Basic)	8.36	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	64.35 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	21.85 m³·mol⁻¹	ChemAxon
Polarizability	8.87 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	118.73	31661259
DarkChem	[M-H]-	113.628	31661259
DeepCCS	[M+H]+	122.195	30932474
DeepCCS	[M-H]-	119.955	30932474
DeepCCS	[M-2H]-	155.8	30932474
DeepCCS	[M+Na]+	130.274	30932474
AllCCS	[M+H]+	122.3	32859911
AllCCS	[M+H-H2O]+	117.3	32859911
AllCCS	[M+NH4]+	126.9	32859911
AllCCS	[M+Na]+	128.3	32859911
AllCCS	[M-H]-	114.2	32859911
AllCCS	[M+Na-2H]-	117.3	32859911
AllCCS	[M+HCOO]-	120.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cycloserine	[H][C@@]1(N)CON=C1O	2209.5	Standard polar	33892256
Cycloserine	[H][C@@]1(N)CON=C1O	1038.6	Standard non polar	33892256
Cycloserine	[H][C@@]1(N)CON=C1O	1276.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cycloserine,1TMS,isomer #1	C[Si](C)(C)OC1=NOC[C@H]1N	1287.6	Semi standard non polar	33892256
Cycloserine,1TMS,isomer #2	C[Si](C)(C)N[C@@H]1CON=C1O	1351.4	Semi standard non polar	33892256
Cycloserine,2TMS,isomer #1	C[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C	1434.8	Semi standard non polar	33892256
Cycloserine,2TMS,isomer #1	C[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C	1535.5	Standard non polar	33892256
Cycloserine,2TMS,isomer #1	C[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C	2443.8	Standard polar	33892256
Cycloserine,2TMS,isomer #2	C[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C	1455.5	Semi standard non polar	33892256
Cycloserine,2TMS,isomer #2	C[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C	1523.8	Standard non polar	33892256
Cycloserine,2TMS,isomer #2	C[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C	2303.8	Standard polar	33892256
Cycloserine,3TMS,isomer #1	C[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C)[Si](C)(C)C	1550.8	Semi standard non polar	33892256
Cycloserine,3TMS,isomer #1	C[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C)[Si](C)(C)C	1622.8	Standard non polar	33892256
Cycloserine,3TMS,isomer #1	C[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C)[Si](C)(C)C	2080.6	Standard polar	33892256
Cycloserine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NOC[C@H]1N	1497.3	Semi standard non polar	33892256
Cycloserine,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N[C@@H]1CON=C1O	1560.4	Semi standard non polar	33892256
Cycloserine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C(C)(C)C	1861.8	Semi standard non polar	33892256
Cycloserine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C(C)(C)C	1895.5	Standard non polar	33892256
Cycloserine,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N[C@@H]1CON=C1O[Si](C)(C)C(C)(C)C	2493.0	Standard polar	33892256
Cycloserine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C(C)(C)C	1815.4	Semi standard non polar	33892256
Cycloserine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C(C)(C)C	1986.7	Standard non polar	33892256
Cycloserine,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)N([C@@H]1CON=C1O)[Si](C)(C)C(C)(C)C	2285.2	Standard polar	33892256
Cycloserine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2122.0	Semi standard non polar	33892256
Cycloserine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2185.4	Standard non polar	33892256
Cycloserine,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1=NOC[C@H]1N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C	2215.6	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Cycloserine GC-MS (2 TMS)	splash10-0uy0-5900000000-06bce0b228f324fe49b4	2014-06-16	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Cycloserine GC-MS (Non-derivatized)	splash10-0uy0-5900000000-06bce0b228f324fe49b4	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cycloserine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9000000000-0e7a5a8b0f7ce48e4509	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cycloserine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 10V, Positive-QTOF	splash10-0udi-4900000000-f1c1692f9e6318f52377	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 20V, Positive-QTOF	splash10-0f79-9300000000-45585d9e68724372ca94	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 40V, Positive-QTOF	splash10-059f-9000000000-bac95a810bc34e20e690	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 10V, Negative-QTOF	splash10-0udi-5900000000-5babaf58090cc358ab6e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 20V, Negative-QTOF	splash10-0f6x-9300000000-0ff851b2ef4ce71985ff	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 40V, Negative-QTOF	splash10-0596-9000000000-8a39f19e4a34080991d1	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 10V, Negative-QTOF	splash10-0udl-9800000000-28ac2fbbebd31cc6100b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 20V, Negative-QTOF	splash10-0006-9200000000-739f88bc4c62ad6e99a6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 40V, Negative-QTOF	splash10-0006-9000000000-90726b17dc36e29c5299	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 10V, Positive-QTOF	splash10-0udi-0900000000-940c87bcfe09a2af1fc9	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 20V, Positive-QTOF	splash10-0w2c-9400000000-13b86532b272b0b5785d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cycloserine 40V, Positive-QTOF	splash10-0006-9000000000-a3d694a542f40615fe9e	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-03	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-03	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00260	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00260	21059682	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00260

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB098104

KNApSAcK ID

Not Available

Chemspider ID

5998

KEGG Compound ID

C08057

BioCyc ID

CPD-2482

BiGG ID

Not Available

Wikipedia Link

Cycloserine

METLIN ID

Not Available

PubChem Compound

6234

PDB ID

4AX

ChEBI ID

40009

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1125331

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Aromatic-L-amino-acid decarboxylase

General function:: Involved in carboxy-lyase activity
Specific function:: Catalyzes the decarboxylation of L-3,4-dihydroxyphenylalanine (DOPA) to dopamine, L-5-hydroxytryptophan to serotonin and L-tryptophan to tryptamine.
Gene Name:: DDC
Uniprot ID:: P20711
Molecular weight:: 53893.755

References

DENGLER HJ, RAUCHS E, RUMMEL W: [On the inhibition of L-glutamic acid and L-DOPA decarboxylase by D-cycloserine and other isoxazolidones]. Naunyn Schmiedebergs Arch Exp Pathol Pharmakol. 1962;243:366-81. [PubMed:13885421 ]

Showing metabocard for Cycloserine (HMDB0014405)

MOL for HMDB0014405 (Cycloserine)

3D MOL for HMDB0014405 (Cycloserine)

3D SDF for HMDB0014405 (Cycloserine)

3D-SDF for HMDB0014405 (Cycloserine)

PDB for HMDB0014405 (Cycloserine)

3D PDB for HMDB0014405 (Cycloserine)

SMILES for HMDB0014405 (Cycloserine)

INCHI for HMDB0014405 (Cycloserine)

Structure for HMDB0014405 (Cycloserine)

3D Structure for HMDB0014405 (Cycloserine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra

Enzymes

References