NP-MRD: Showing NP-Card for Cystathionine ketimine (NP0086841)

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Record Information

Version

2.0

Created at

2022-05-11 16:32:30 UTC

Updated at

2022-05-11 16:32:30 UTC

NP-MRD ID

NP0086841

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cystathionine ketimine

Description

Cystathionine ketimine, also known as CT, 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. Among the cystathionine metabolites, cystathionine ketimine and N-acetyl-S-(3-oxo-3-carboxy-n-propyl) cysteine (NAc-OCPC) significantly enhanced the N-formylmethionylleucylphenylalanine (fMLP)-induced superoxide generation, but cystathionine, NAc-cystathionine, and cyclothionine did not enhance the superoxide generation. Cystathionine ketimine is an extremely weak basic (essentially neutral) compound (based on its pKa). Superoxide generation induced by cystathionine ketimine and NAc-OCPC was inhibited by genistein, an inhibitor of tyrosine kinase, and was enhanced by 1-(5-isoquinoline sulfonyl)-2-methylpiperazine (H-7), an inhibitor of protein kinase C. D-cystathionine ketimine and L-cystathionine ketimine enhance superoxide generation by human neutrophils in a different manner. Cystathionine ketimine was found in the urine of a cystathioninuria patient (PMID: 8373176 ). D-Cystathionine ketimine and L-cystathionine ketimine enhance superoxide generation by human neutrophils in two different manners. Cystathionine ketimine was first documented in 1988 (PMID: 3254164). Cystathionine ketimine (CT) is a cyclic amino acid that was found to have a priming effeCystathionine ketimine on superoxide generation in human neutrophils (PMID: 10708546 ) (PMID: 8373176) (PMID: 2361849) (PMID: 10049498) (PMID: 10708546).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231219192D          

 13 13  0  0  1  0            999 V2000
   17.9424   -3.4365    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   15.3736   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6862   -5.0988    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2646   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7953   -6.2159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5299   -5.2437    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.7865   -4.8858    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.1174   -3.4365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6031   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4568   -4.0816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1415   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9182   -5.4002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.2732   -4.8858    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  8  1  0  0  0  0
  1 10  1  0  0  0  0
  2 11  1  0  0  0  0
  3 12  1  0  0  0  0
  4 11  2  0  0  0  0
  5 12  2  0  0  0  0
  6  7  1  0  0  0  0
  6 13  2  0  0  0  0
  7  9  1  0  0  0  0
  7 11  1  1  0  0  0
  8  9  1  0  0  0  0
 10 13  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0086841

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@H]1CCSCC(=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H9NO4S/c9-6(10)4-1-2-13-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m1/s1

> <INCHI_KEY>
XJUQJVUYGRTQGI-SCSAIBSYSA-N

> <FORMULA>
C7H9NO4S

> <MOLECULAR_WEIGHT>
203.216

> <EXACT_MASS>
203.025228471

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
18.442346082610634

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R)-2,5,6,7-tetrahydro-1,4-thiazepine-3,5-dicarboxylic acid

> <ALOGPS_LOGP>
-0.09

> <JCHEM_LOGP>
0.3903825910000002

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.9664414229319367

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2398428110676822

> <JCHEM_PKA_STRONGEST_BASIC>
-2.2790816811427703

> <JCHEM_POLAR_SURFACE_AREA>
86.96

> <JCHEM_REFRACTIVITY>
46.199200000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.81e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cystathionine ketimine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  S   UNK     0      33.492  -6.415   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      28.697  -9.518   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      36.748  -9.518   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      30.361 -11.603   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      35.085 -11.603   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0      32.722  -9.788   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      31.335  -9.120   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      31.952  -6.415   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      30.992  -7.619   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      34.453  -7.619   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      30.131 -10.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      35.314 -10.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      34.110  -9.120   0.000  0.00  0.00           C+0
CONECT    1    8   10                                                       
CONECT    2   11                                                            
CONECT    3   12                                                            
CONECT    4   11                                                            
CONECT    5   12                                                            
CONECT    6    7   13                                                       
CONECT    7    6    9   11                                                  
CONECT    8    1    9                                                       
CONECT    9    7    8                                                       
CONECT   10    1   13                                                       
CONECT   11    2    4    7                                                  
CONECT   12    3    5   13                                                  
CONECT   13    6   10   12                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol

Synonyms

Value	Source
(5R)-2,5,6,7-Tetrahydro-1,4-thiazepine-3,5-dicarboxylic acid	HMDB
(5R)-2,5,6,7-Tetrahydro-1,4-thiazepine-3,5-dicarboxylate	HMDB
CT	HMDB
Cystathionine ketimine	MeSH

Chemical Formula

C₇H₉NO₄S

Average Mass

203.2160 Da

Monoisotopic Mass

203.02523 Da

IUPAC Name

(5R)-2,5,6,7-tetrahydro-1,4-thiazepine-3,5-dicarboxylic acid

Traditional Name

cystathionine ketimine

CAS Registry Number

Not Available

SMILES

OC(=O)[C@H]1CCSCC(=N1)C(O)=O

InChI Identifier

InChI=1S/C7H9NO4S/c9-6(10)4-1-2-13-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m1/s1

InChI Key

XJUQJVUYGRTQGI-SCSAIBSYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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
Dicarboxylic acid or derivatives
Ketimine
Carboxylic acid
Thioether
Azacycle
Organoheterocyclic compound
Dialkylthioether
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Imine
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-0.09	ALOGPS
logP	0.39	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	-2.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	86.96 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	46.2 m³·mol⁻¹	ChemAxon
Polarizability	18.44 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0002015

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022797

KNApSAcK ID

Not Available

Chemspider ID

119692

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6438

PubChem Compound

135905

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pecci L, Antonucci A, Nardini M, Cavallini D: Detection of cystathionine and lanthionine ketimines in human urine. Biochem Int. 1988 Nov;17(5):877-83. [PubMed:3254164 ]
Okada T, Takechi T, Wakiguchi H, Kurashige T, Sugahara K, Kodama H: Identification of new cystathionine mono-oxo acids, S-(3-oxo-3-carboxy-n-propyl) cysteine and S-(2-oxo-2-carboxyethyl) homocysteine, in the urine of a patient with cystathioninuria. Arch Biochem Biophys. 1993 Sep;305(2):385-91. doi: 10.1006/abbi.1993.1436. [PubMed:8373176 ]
Antonucci A, Pecci L, Fontana M, Cavallini D: Influence of diet on cystathionine ketimine and lanthionine ketimine content in human urine. Ital J Biochem. 1990 Mar-Apr;39(2):100-5. [PubMed:2361849 ]
Zhang J, Zhang M, Sugahara K, Sagara Y, Spirito A, Dupre, Kodama H: D-cystathionine ketimine and L-cystathionine ketimine enhance superoxide generation by human neutrophils in a different manner. Arch Biochem Biophys. 1999 Mar 1;363(1):55-9. doi: 10.1006/abbi.1998.1063. [PubMed:10049498 ]
Kodama H, Zhang J, Sugahara K: Novel priming compounds of cystathionine metabolites on superoxide generation in human neutrophils. Biochem Biophys Res Commun. 2000 Mar 16;269(2):297-301. doi: 10.1006/bbrc.1999.1970. [PubMed:10708546 ]

Showing NP-Card for Cystathionine ketimine (NP0086841)

MOL for NP0086841 (Cystathionine ketimine)

3D MOL for NP0086841 (Cystathionine ketimine)

3D SDF for NP0086841 (Cystathionine ketimine)

3D-SDF for NP0086841 (Cystathionine ketimine)

PDB for NP0086841 (Cystathionine ketimine)

3D PDB for NP0086841 (Cystathionine ketimine)

SMILES for NP0086841 (Cystathionine ketimine)

INCHI for NP0086841 (Cystathionine ketimine)

Structure for NP0086841 (Cystathionine ketimine)

3D Structure for NP0086841 (Cystathionine ketimine)