NP-MRD: Showing NP-Card for O-Succinyl-L-homoserine (NP0002606)

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Record Information

Version

1.0

Created at

2020-11-23 18:25:07 UTC

Updated at

2021-08-12 19:51:38 UTC

NP-MRD ID

NP0002606

Secondary Accession Numbers

None

Natural Product Identification

Common Name

O-Succinyl-L-homoserine

Provided By

BMRB

Description

O-succinyl-L-homoserine belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. O-Succinyl-L-homoserine is found in Apis cerana, Daphnia pulex and Paraburkholderia phymatum. It was first documented in 1990 (PMID: 2405903). Based on a literature review a significant number of articles have been published on O-succinyl-L-homoserine (PMID: 17984079) (PMID: 29565828) (PMID: 14607989) (PMID: 22855027).

Structure

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

 
  Mrv1652303062005542D          

 15 14  0  0  1  0            999 V2000
   27.6994  -16.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4149  -16.3531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6994  -17.5937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1341  -16.7640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.8497  -16.3531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5650  -16.7640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   31.2843  -16.3492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5688  -17.5937    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   31.9998  -16.7640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.2843  -15.6482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9879  -16.3581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2886  -16.7628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5941  -16.3627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8987  -16.7651    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5932  -15.5410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  1  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  1 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0002606

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](CCOC(=O)CCC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO6/c9-5(8(13)14)3-4-15-7(12)2-1-6(10)11/h5H,1-4,9H2,(H,10,11)(H,13,14)/t5-/m0/s1

> <INCHI_KEY>
GNISQJGXJIDKDJ-YFKPBYRVSA-N

> <FORMULA>
C8H13NO6

> <MOLECULAR_WEIGHT>
219.1919

> <EXACT_MASS>
219.074287153

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.513811131589183

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-[(3-carboxypropanoyl)oxy]butanoic acid

> <ALOGPS_LOGP>
-3.31

> <JCHEM_LOGP>
-3.6100642791309556

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.112459497104107

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.688067433289202

> <JCHEM_PKA_STRONGEST_BASIC>
9.458196258009957

> <JCHEM_POLAR_SURFACE_AREA>
126.92000000000002

> <JCHEM_REFRACTIVITY>
46.95120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
O-succinyl-L-homoserine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0      51.706 -31.300   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      53.041 -30.526   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      51.706 -32.842   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      54.384 -31.293   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      55.719 -30.526   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      57.055 -31.293   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      58.397 -30.518   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      57.062 -32.842   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      59.733 -31.293   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      58.397 -29.210   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      50.377 -30.535   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      49.072 -31.291   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      47.776 -30.544   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      46.478 -31.295   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      47.774 -29.010   0.000  0.00  0.00           O+0
CONECT    1    2    3   11                                                  
CONECT    2    1    4                                                       
CONECT    3    1                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6    9   10                                                  
CONECT    8    6                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11    1   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

COMPND    NP0002606
HETATM    1  N1  UNL     1      -3.456   1.897   0.934  1.00  0.00           N  
HETATM    2  C1  UNL     1      -2.968   0.906  -0.025  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.562   0.599   0.307  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.881  -0.406  -0.591  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.444  -0.520  -0.076  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.372  -1.344  -0.694  1.00  0.00           C  
HETATM    7  O2  UNL     1       0.976  -1.956  -1.703  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.728  -1.417  -0.109  1.00  0.00           C  
HETATM    9  C6  UNL     1       3.463  -0.146  -0.548  1.00  0.00           C  
HETATM   10  C7  UNL     1       4.836  -0.135  -0.015  1.00  0.00           C  
HETATM   11  O3  UNL     1       5.242  -1.118   0.647  1.00  0.00           O  
HETATM   12  O4  UNL     1       5.667   0.957  -0.246  1.00  0.00           O  
HETATM   13  C8  UNL     1      -3.891  -0.209  -0.152  1.00  0.00           C  
HETATM   14  O5  UNL     1      -3.713  -1.201  -0.880  1.00  0.00           O  
HETATM   15  O6  UNL     1      -5.086  -0.178   0.604  1.00  0.00           O  
HETATM   16  H1  UNL     1      -2.886   1.867   1.808  1.00  0.00           H  
HETATM   17  H2  UNL     1      -4.462   1.712   1.192  1.00  0.00           H  
HETATM   18  H3  UNL     1      -2.955   1.466  -1.008  1.00  0.00           H  
HETATM   19  H4  UNL     1      -0.916   1.502   0.302  1.00  0.00           H  
HETATM   20  H5  UNL     1      -1.462   0.179   1.354  1.00  0.00           H  
HETATM   21  H6  UNL     1      -0.845  -0.106  -1.648  1.00  0.00           H  
HETATM   22  H7  UNL     1      -1.392  -1.405  -0.579  1.00  0.00           H  
HETATM   23  H8  UNL     1       3.292  -2.312  -0.447  1.00  0.00           H  
HETATM   24  H9  UNL     1       2.686  -1.384   0.996  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.870   0.725  -0.190  1.00  0.00           H  
HETATM   26  H11 UNL     1       3.503  -0.180  -1.646  1.00  0.00           H  
HETATM   27  H12 UNL     1       5.322   1.927  -0.222  1.00  0.00           H  
HETATM   28  H13 UNL     1      -5.927   0.282   0.273  1.00  0.00           H  
CONECT    1    2   16   17
CONECT    2    3   13   18
CONECT    3    4   19   20
CONECT    4    5   21   22
CONECT    5    6
CONECT    6    7    7    8
CONECT    8    9   23   24
CONECT    9   10   25   26
CONECT   10   11   11   12
CONECT   12   27
CONECT   13   14   14   15
CONECT   15   28
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
O-Succinylhomoserine	ChEBI
O4-Succinyl-L-homoserine	ChEBI
O-Succinylhomoserine, (DL)-isomer	MeSH

Chemical Formula

C₈H₁₃NO₆

Average Mass

219.1919 Da

Monoisotopic Mass

219.07429 Da

IUPAC Name

(2S)-2-amino-4-[(3-carboxypropanoyl)oxy]butanoic acid

Traditional Name

O-succinyl-L-homoserine

CAS Registry Number

Not Available

SMILES

N[C@@H](CCOC(=O)CCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C8H13NO6/c9-5(8(13)14)3-4-15-7(12)2-1-6(10)11/h5H,1-4,9H2,(H,10,11)(H,13,14)/t5-/m0/s1

InChI Key

GNISQJGXJIDKDJ-YFKPBYRVSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View

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	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, 176 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	¹H NMR Spectrum (1D, 900 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

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633
Daphnia pulex	LOTUS Database	35616633
Paraburkholderia phymatum	-	KNApSAcK

Species Where Detected

Species Name	Source	Reference
Escherichia coli K12	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aliphatic acyclic 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	-3.3	ALOGPS
logP	-3.6	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.69	ChemAxon
pKa (Strongest Basic)	9.46	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	126.92 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	46.95 m³·mol⁻¹	ChemAxon
Polarizability	20.51 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

O-SUCCINYL-L-HOMOSERINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

16160

Good Scents ID

Not Available

References

General References

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]
Yamagata S, Yasugahira T, Okuda Y, Iwama T: Conversion of the aminocrotonate intermediate limits the rate of gamma-elimination reaction catalyzed by L-cystathionine gamma-lyase of the yeast Saccharomyces cerevisiae. J Biochem. 2003 Oct;134(4):607-13. doi: 10.1093/jb/mvg179. [PubMed:14607989 ]
Jaworski AF, Lodha PH, Manders AL, Aitken SM: Exploration of the active site of Escherichia coli cystathionine gamma-synthase. Protein Sci. 2012 Nov;21(11):1662-71. doi: 10.1002/pro.2135. [PubMed:22855027 ]
Holbrook EL, Greene RC, Krueger JH: Purification and properties of cystathionine gamma-synthase from overproducing strains of Escherichia coli. Biochemistry. 1990 Jan 16;29(2):435-42. doi: 10.1021/bi00454a019. [PubMed:2405903 ]

Showing NP-Card for O-Succinyl-L-homoserine (NP0002606)

MOL for NP0002606 (O-Succinyl-L-homoserine)

3D MOL for NP0002606 (O-Succinyl-L-homoserine)

3D SDF for NP0002606 (O-Succinyl-L-homoserine)

3D-SDF for NP0002606 (O-Succinyl-L-homoserine)

PDB for NP0002606 (O-Succinyl-L-homoserine)

3D PDB for NP0002606 (O-Succinyl-L-homoserine)

SMILES for NP0002606 (O-Succinyl-L-homoserine)

INCHI for NP0002606 (O-Succinyl-L-homoserine)

Structure for NP0002606 (O-Succinyl-L-homoserine)

3D Structure for NP0002606 (O-Succinyl-L-homoserine)