NP-MRD: Showing NP-Card for 2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid (NP0209914)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-05 07:31:00 UTC

Updated at

2022-09-05 07:31:00 UTC

NP-MRD ID

NP0209914

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid

Description

Lombricine belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Lombricine is a very strong basic compound (based on its pKa). 2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid is found in Apis cerana. 2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid was first documented in 1959 (PMID: 13632801). A serine derivative that is serine in which the hydrogen of the hydroxy group has been replaced by a (2-carbamimidamidoethoxy)(hydroxy)phosphoryl group (PMID: 14439305) (PMID: 1909513) (PMID: 22705027).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 31  0  0  0  0  0  0  0  0999 V2000
    5.6102    1.8977    1.0514 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8235    1.2673    0.9654 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5749    0.2336    0.2812 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5734   -0.2347   -0.5915 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3389   -0.4489    0.3987 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6161   -0.7196   -0.7753 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2324   -1.2486   -0.7207 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5704   -0.3209    0.1023 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    0.3716   -0.7318 P   0  0  2  0  0  5  0  0  0  0  0  0
   -0.1336    0.7409   -2.1797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7325    1.9664    0.0725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1699   -0.1635   -0.6581 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5612   -0.3550    0.6452 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0790   -0.2201    0.6223 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7787   -1.2990    0.0236 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2103    0.9382   -0.4562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2220    0.5704   -1.6031 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3126    2.2044    0.0143 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7705   -1.2787   -0.4822 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1086    0.2226   -1.2780 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0737   -0.7583    1.3642 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2528   -1.2925   -1.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5636    0.3458   -1.2784 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1206   -2.2847   -0.4601 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8279   -1.0921   -1.7809 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2371    2.1762    0.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3205   -1.4895    0.8478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0657    0.1699    1.4307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4724    0.2277    1.5343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8031   -2.1330    0.7282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8482   -1.0172   -0.0443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9563    3.0238   -0.4398 H   0  0  0  0  0  0  0  0  0  0  0  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
  9 12  1  6
  9 11  1  0
  9 10  2  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 14 16  1  0
 16 18  1  0
 16 17  2  0
 15 30  1  0
 15 31  1  0
 14 29  1  1
 13 27  1  0
 13 28  1  0
 11 26  1  0
  7 24  1  0
  7 25  1  0
  6 22  1  0
  6 23  1  0
  5 21  1  0
  4 19  1  0
  4 20  1  0
  2  1  1  0
 18 32  1  0
M  END


  Mrv1533004161519242D          

 17 16  0  0  0  0            999 V2000
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    2.8579    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    4.2868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    5.7158    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    6.4302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    7.1447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    6.4302    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0209914

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(COP(O)(=O)OCCNC(N)=N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H15N4O6P/c7-4(5(11)12)3-16-17(13,14)15-2-1-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H,13,14)(H4,8,9,10)

> <INCHI_KEY>
GSDBGCKBBJVPNC-UHFFFAOYSA-N

> <FORMULA>
C6H15N4O6P

> <MOLECULAR_WEIGHT>
270.182

> <EXACT_MASS>
270.072921217

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.130454139006876

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-3-{[(2-carbamimidamidoethoxy)(hydroxy)phosphoryl]oxy}propanoic acid

> <ALOGPS_LOGP>
-3.37

> <JCHEM_LOGP>
-8.194853460875631

> <ALOGPS_LOGS>
-1.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
2.2990863238615593

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5834941777580411

> <JCHEM_PKA_STRONGEST_BASIC>
11.772520168292619

> <JCHEM_POLAR_SURFACE_AREA>
180.98

> <JCHEM_REFRACTIVITY>
66.06060000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.99e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310   4.001   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0       1.540   5.335   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0       0.206   4.565   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.874   6.105   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.770   6.668   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.540   8.002   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.770   9.336   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       1.540  10.669   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       0.770  12.003   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.540  13.337   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -0.770  12.003   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    2   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₆H₁₅N₄O₆P

Average Mass

270.1820 Da

Monoisotopic Mass

270.07292 Da

IUPAC Name

2-amino-3-{[(2-carbamimidamidoethoxy)(hydroxy)phosphoryl]oxy}propanoic acid

Traditional Name

2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid

CAS Registry Number

Not Available

SMILES

NC(COP(O)(=O)OCCNC(N)=N)C(O)=O

InChI Identifier

InChI=1S/C6H15N4O6P/c7-4(5(11)12)3-16-17(13,14)15-2-1-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H,13,14)(H4,8,9,10)

InChI Key

GSDBGCKBBJVPNC-UHFFFAOYSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).

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

Alternative Parents

Substituents

Alpha-amino acid
Phosphoethanolamine
Dialkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Guanidine
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Carboximidamide
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic oxide
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Organic nitrogen compound
Primary aliphatic amine
Organic oxygen compound
Hydrocarbon derivative
Primary amine
Amine
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

guanidines (CHEBI:25072 )
O-phosphoamino acid (CHEBI:25072 )
serine derivative (CHEBI:25072 )

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	-3.4	ALOGPS
logP	-8.2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	1.58	ChemAxon
pKa (Strongest Basic)	11.77	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	180.98 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	66.06 m³·mol⁻¹	ChemAxon
Polarizability	23.13 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Lombricine

METLIN ID

Not Available

PubChem Compound

4475104

PDB ID

Not Available

ChEBI ID

25072

Good Scents ID

Not Available

References

General References

BEATTY IM, MAGRATH DI, ENNOR AH: Occurrence of D-serine in lombricine. Nature. 1959 Feb 28;183(4661):591. doi: 10.1038/183591a0. [PubMed:13632801 ]
ROSSITER RJ, GAFFNEY T, ROSENBERG H, ENNOR AH: Biosynthesis of lombricine. Nature. 1960 Feb 6;185:383-4. doi: 10.1038/185383a0. [PubMed:14439305 ]
Nagasawa H, Sawaki K, Fujii Y, Kobayashi M, Segawa T, Suzuki R, Inatomi H: Inhibition by lombricine from earthworm (Lumbricus terrestris) of the growth of spontaneous mammary tumours in SHN mice. Anticancer Res. 1991 May-Jun;11(3):1061-4. [PubMed:1909513 ]
Doumen C: Variable intron/exon structure in the oligochaete lombricine kinase gene. Gene. 2012 Sep 1;505(2):276-82. doi: 10.1016/j.gene.2012.06.007. Epub 2012 Jun 12. [PubMed:22705027 ]
LOTUS database [Link]

Showing NP-Card for 2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid (NP0209914)

MOL for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

3D MOL for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

3D SDF for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

3D-SDF for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

PDB for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

3D PDB for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

SMILES for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

INCHI for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

Structure for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)

3D Structure for NP0209914 (2-amino-3-{[2-carbamimidamidoethoxy(hydroxy)phosphoryl]oxy}propanoic acid)