Showing NP-Card for D-Cycloserine (NP0137396)

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Record Information
Version2.0
Created at2022-05-30 16:51:16 UTC
Updated at2022-05-30 16:51:16 UTC
NP-MRD IDNP0137396
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Cycloserine
DescriptionCycloserine, also known as alpha-cycloserine or seromycin, 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. Thus, cycloserine is considered to be a non-ribosomal peptide/polyketide hybrid lipid molecule. Cycloserine is a drug which is used in combination with up to 5 other drugs as a treatment for mycobacterium avium complex (mac) and is also used to treat tuberculosis (tb). D-Cycloserine is found in Streptomyces garyphalus and Streptomyces lavendulae. D-Cycloserine was first documented in 2002 (PMID: 12076471). Cycloserine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (PMID: 17707326) (PMID: 18316423) (PMID: 18486041).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0137396 (D-Cycloserine)

  Mrv1652304032018302D          

  8  8  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  4  1  6  0  0  0
  5  3  2  0  0  0  0
  6  3  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  2  8  1  1  0  0  0
M  END
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3D MOL for NP0137396 (D-Cycloserine)

     RDKit          3D

 13 13  0  0  0  0  0  0  0  0999 V2000
   -0.9141   -1.2199   -0.5478 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4179   -0.1389    0.2568 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5475    1.2072   -0.4198 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3984    1.9254    0.3985 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4571    1.0281    0.5459 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0419   -0.1835    0.4717 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8546   -1.3223    0.5795 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7774   -0.8801   -1.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2950   -1.9498    0.1220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9818   -0.0774    1.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5462    1.6378   -0.3674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0961    1.2131   -1.4382 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8241   -1.2398    0.2581 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  6  2  1  0
  2 10  1  1
  1  8  1  0
  1  9  1  0
  3 11  1  0
  3 12  1  0
  7 13  1  0
M  END
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3D SDF for NP0137396 (D-Cycloserine)

  Mrv1652304032018302D          

  8  8  0  0  1  0            999 V2000
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  2  4  1  6  0  0  0
  5  3  2  0  0  0  0
  6  3  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  2  8  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0137396

> <DATABASE_NAME>
NP-MRD

> <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

> <FORMULA>
C3H6N2O2

> <MOLECULAR_WEIGHT>
102.0919

> <EXACT_MASS>
102.042927446

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.866828047891495

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.33

> <JCHEM_LOGP>
-2.421332341545318

> <ALOGPS_LOGS>
-0.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.998851660051976

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.210086895651751

> <JCHEM_PKA_STRONGEST_BASIC>
8.361863652158748

> <JCHEM_POLAR_SURFACE_AREA>
64.35

> <JCHEM_REFRACTIVITY>
21.848800000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.19e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cycloserine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0137396 (D-Cycloserine)

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PDB for NP0137396 (D-Cycloserine)
HEADER    PROTEIN                                 03-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-APR-20         0                                  
HETATM    1  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0       0.290  -0.290   0.000  0.00  0.00           N+0
HETATM    6  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1    3    4    8                                             
CONECT    3    2    5    6                                                  
CONECT    4    2                                                            
CONECT    5    3    7                                                       
CONECT    6    3                                                            
CONECT    7    1    5                                                       
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0137396 (D-Cycloserine)
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SMILES for NP0137396 (D-Cycloserine)
[H][C@@]1(N)CON=C1O
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INCHI for NP0137396 (D-Cycloserine)
InChI=1S/C3H6N2O2/c4-2-1-7-5-3(2)6/h2H,1,4H2,(H,5,6)/t2-/m1/s1
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Synonyms
Chemical FormulaC3H6N2O2
Average Mass102.0919 Da
Monoisotopic Mass102.04293 Da
IUPAC Name(4R)-4-amino-1,2-oxazolidin-3-one
Traditional Namecycloserine
CAS Registry NumberNot Available
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 KeyDYDCUQKUCUHJBH-UWTATZPHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces garyphalusLOTUS Database
Streptomyces lavendulaeLOTUS Database
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.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassAzolines  
Sub ClassIsoxazolines  
Direct ParentIsoxazolines  
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 FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.3ALOGPS
logP-2.4ChemAxon
logS-0.15ALOGPS
pKa (Strongest Acidic)4.21ChemAxon
pKa (Strongest Basic)8.36ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area64.35 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity21.85 m³·mol⁻¹ChemAxon
Polarizability8.87 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0014405  
DrugBank IDDB00260  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5998  
KEGG Compound IDC08057  
BioCyc IDCPD-2482  
BiGG IDNot Available
Wikipedia LinkCycloserine  
METLIN IDNot Available
PubChem Compound6234  
PDB ID4AX  
ChEBI ID40009  
Good Scents IDNot Available
References
General References
  1. Laake K, Oeksengaard AR: D-cycloserine for Alzheimer's disease. Cochrane Database Syst Rev. 2002;(2):CD003153. doi: 10.1002/14651858.CD003153. [PubMed:12076471  ] 
  2. Vervliet B: Learning and memory in conditioned fear extinction: effects of D-cycloserine. Acta Psychol (Amst). 2008 Mar;127(3):601-13. doi: 10.1016/j.actpsy.2007.07.001. Epub 2007 Aug 17. [PubMed:17707326  ] 
  3. Rothbaum BO: Critical parameters for D-cycloserine enhancement of cognitive-behaviorial therapy for obsessive-compulsive disorder. Am J Psychiatry. 2008 Mar;165(3):293-6. doi: 10.1176/appi.ajp.2007.07121871. [PubMed:18316423  ] 
  4. Authors unspecified: Cycloserine. Tuberculosis (Edinb). 2008 Mar;88(2):100-1. doi: 10.1016/S1472-9792(08)70007-6. [PubMed:18486041  ]