NP-MRD: Showing NP-Card for {[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid (NP0150921)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2022-09-02 07:09:34 UTC

Updated at

2022-09-02 07:09:35 UTC

NP-MRD ID

NP0150921

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid

Description

2-{[(3,6-Diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta carbon atom. 2-{[(3,6-Diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 36  0  0  0  0  0  0  0  0999 V2000
    4.1072   -1.2981   -0.7236 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1925   -0.2097   -0.3740 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3168    0.1119    1.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6437    0.7087    1.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0104    1.0811    2.4040 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5134    0.8701    0.1926 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8987   -0.6390   -0.6104 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8183    0.2587   -0.4919 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9597    1.4645   -0.1729 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5538   -0.2379   -0.7541 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5342    0.8762   -0.4946 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1746    1.9665   -1.4106 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9366    0.4519   -0.8856 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3327   -0.7471   -0.0899 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6251   -1.1716   -0.4252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1695   -0.5436    1.3792 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0604    0.4442    1.9330 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5775   -1.0531   -1.6936 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8244   -1.4908    0.0925 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5169   -2.2453   -0.9036 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5705    0.8558    1.3651 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1487   -0.7908    1.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2270    1.3059   -0.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7218   -1.6204   -0.8728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7197   -1.1022   -0.0594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6645   -0.6362   -1.7864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4606    1.2048    0.5503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9561    2.6254   -1.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8400    1.5223   -2.2761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9447    0.2656   -1.9737 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5940    1.3345   -0.6970 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6645   -1.6012   -0.3715 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6298   -1.9773   -0.9945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4635   -1.5203    1.8612 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1503   -0.3212    1.6932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9591    0.5341    1.4129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6138    1.3236    2.2117 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  6  1  0
  4  5  2  0
  2  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  6 23  1  0
  7 24  1  0
 10 25  1  0
 10 26  1  0
 11 27  1  1
 12 28  1  0
 12 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  0
 16 35  1  0
 17 36  1  0
 17 37  1  0
M  END


  Mrv1533004161505112D          

 17 16  0  0  0  0            999 V2000
    5.6645    4.0954    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645    3.2704    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5211    2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355    4.0954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3789    2.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0934    4.0954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5224    4.0954    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2368    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    3.2704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9513    4.0954    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6658    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3802    3.2704    0.0000 N   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  2  0  0  0  0
  4  6  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0150921

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(CC(O)=O)NC(=O)CC(N)CC(O)CN

> <INCHI_IDENTIFIER>
InChI=1S/C9H20N4O4/c1-13(5-9(16)17)12-8(15)3-6(11)2-7(14)4-10/h6-7,14H,2-5,10-11H2,1H3,(H,12,15)(H,16,17)

> <INCHI_KEY>
IKHFJPZQZVMLRH-UHFFFAOYSA-N

> <FORMULA>
C9H20N4O4

> <MOLECULAR_WEIGHT>
248.283

> <EXACT_MASS>
248.14845514

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.049941796266232

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3,6-diamino-5-hydroxy-N'-methylhexanehydrazido)acetic acid

> <ALOGPS_LOGP>
-3.60

> <JCHEM_LOGP>
-6.230302715651079

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.479776826981986

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.016318310366975

> <JCHEM_PKA_STRONGEST_BASIC>
9.685453997096024

> <JCHEM_POLAR_SURFACE_AREA>
141.91000000000003

> <JCHEM_REFRACTIVITY>
60.1509

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.52e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,6-diamino-5-hydroxy-N'-methylhexanehydrazido)acetic 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  C   UNK     0      10.574   7.645   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      10.574   6.105   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       9.240   5.335   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.906   6.105   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.573   5.335   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       7.906   7.645   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      11.907   5.335   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      13.241   6.105   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      13.241   7.645   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      14.575   5.335   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.908   6.105   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      15.908   7.645   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      17.242   5.335   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      18.576   6.105   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      18.576   7.645   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      21.243   6.105   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

View in JSmol

Synonyms

Value	Source
2-{[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetate	Generator

Chemical Formula

C₉H₂₀N₄O₄

Average Mass

248.2830 Da

Monoisotopic Mass

248.14846 Da

IUPAC Name

2-(3,6-diamino-5-hydroxy-N'-methylhexanehydrazido)acetic acid

Traditional Name

(3,6-diamino-5-hydroxy-N'-methylhexanehydrazido)acetic acid

CAS Registry Number

Not Available

SMILES

CN(CC(O)=O)NC(=O)CC(N)CC(O)CN

InChI Identifier

InChI=1S/C9H20N4O4/c1-13(5-9(16)17)12-8(15)3-6(11)2-7(14)4-10/h6-7,14H,2-5,10-11H2,1H3,(H,12,15)(H,16,17)

InChI Key

IKHFJPZQZVMLRH-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta amino acids and derivatives. These are amino acids having a (-NH2) group attached to the beta 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

Beta amino acids and derivatives

Alternative Parents

Substituents

Beta amino acid or derivatives
Alpha-amino acid or derivatives
1,3-aminoalcohol
1,2-aminoalcohol
Amino acid
Carboxylic acid hydrazide
Secondary alcohol
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Primary aliphatic amine
Primary amine
Hydrocarbon derivative
Carbonyl group
Organic oxide
Amine
Organopnictogen compound
Alcohol
Organic oxygen compound
Aliphatic acyclic compound

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	-3.6	ALOGPS
logP	-6.2	ChemAxon
logS	-0.99	ALOGPS
pKa (Strongest Acidic)	4.02	ChemAxon
pKa (Strongest Basic)	9.69	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	141.91 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	60.15 m³·mol⁻¹	ChemAxon
Polarizability	25.05 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

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

Not Available

METLIN ID

Not Available

PubChem Compound

36458

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid (NP0150921)

MOL for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

3D MOL for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

3D SDF for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

3D-SDF for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

PDB for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

3D PDB for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

SMILES for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

INCHI for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

Structure for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)

3D Structure for NP0150921 ({[(3,6-diamino-1,5-dihydroxyhexylidene)amino](methyl)amino}acetic acid)