NP-MRD: Showing NP-Card for {[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid (NP0276050)

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Record Information

Version

1.0

Created at

2022-09-09 00:00:06 UTC

Updated at

2022-09-09 00:00:06 UTC

NP-MRD ID

NP0276050

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

SCHEMBL11880670 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. {[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid is found in Streptomyces goshikiensis. SCHEMBL11880670 is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 35  0  0  0  0  0  0  0  0999 V2000
    4.6041   -1.0782   -0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4115   -0.3422    0.1823 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5930    0.9689    0.6292 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1335    1.8847   -0.4298 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2841    3.0964   -0.1617 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691    1.4328   -1.6873 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2910   -1.0408    0.3550 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9892   -0.4999    0.2538 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8507    0.7146   -0.0127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2332   -1.3367    0.4580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4387   -0.4023    0.4086 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5217    0.2573   -0.8574 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6946   -1.1074    0.7493 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8956   -0.2367    0.7372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2757    0.4079   -0.5638 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5353    1.1753   -0.3681 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7689   -1.1055   -1.1984 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4819   -2.1220    0.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4767   -0.6486    0.4367 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3587    1.0328    1.4758 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6754    1.4187    1.0097 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8644    1.6420   -2.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3230   -2.0824    0.5765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1847   -1.8914    1.3850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2607   -2.0519   -0.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2476    0.3318    1.2506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7984   -0.1518   -1.4906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2397    1.2699   -0.7170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6174   -1.5757    1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8984   -1.9484    0.0103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7917   -0.7550    1.2056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7631    0.6500    1.4495 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4227   -0.3573   -1.3437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5524    1.1825   -0.8671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3961    2.1647   -0.6153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8074    1.1038    0.6252 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
 15 16  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  6 22  1  0
  7 23  1  0
 10 24  1  0
 10 25  1  0
 11 26  1  1
 12 27  1  0
 12 28  1  0
 13 29  1  0
 13 30  1  0
 14 31  1  0
 14 32  1  0
 15 33  1  0
 15 34  1  0
 16 35  1  0
 16 36  1  0
M  END


  Mrv1533004201502302D          

 16 15  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
   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
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0276050

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H20N4O3/c1-13(6-9(15)16)12-8(14)5-7(11)3-2-4-10/h7H,2-6,10-11H2,1H3,(H,12,14)(H,15,16)

> <INCHI_KEY>
GMDVGRCKPKMEFK-UHFFFAOYSA-N

> <FORMULA>
C9H20N4O3

> <MOLECULAR_WEIGHT>
232.284

> <EXACT_MASS>
232.15354052

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
24.39466642663921

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-3.38

> <JCHEM_LOGP>
-5.023806031058204

> <ALOGPS_LOGS>
-1.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.64936034713612

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.2462677457217115

> <JCHEM_PKA_STRONGEST_BASIC>
10.259369038446312

> <JCHEM_POLAR_SURFACE_AREA>
121.68

> <JCHEM_REFRACTIVITY>
58.833000000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.13e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,6-diamino-N'-methylhexanehydrazido)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-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  C   UNK     0      19.909   5.335   0.000  0.00  0.00           C+0
HETATM   16  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                                                       
CONECT   15   14   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₉H₂₀N₄O₃

Average Mass

232.2840 Da

Monoisotopic Mass

232.15354 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H20N4O3/c1-13(6-9(15)16)12-8(14)5-7(11)3-2-4-10/h7H,2-6,10-11H2,1H3,(H,12,14)(H,15,16)

InChI Key

GMDVGRCKPKMEFK-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
Streptomyces goshikiensis	LOTUS Database	35616633

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
Carboxylic acid hydrazide
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Amine
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	-3.4	ALOGPS
logP	-5	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	4.25	ChemAxon
pKa (Strongest Basic)	10.26	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	121.68 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	58.83 m³·mol⁻¹	ChemAxon
Polarizability	24.39 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

23621249

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-hydroxyhexylidene)amino](methyl)amino}acetic acid (NP0276050)

MOL for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

3D MOL for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

3D SDF for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

3D-SDF for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

PDB for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

3D PDB for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

SMILES for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

INCHI for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

Structure for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)

3D Structure for NP0276050 ({[(3,6-diamino-1-hydroxyhexylidene)amino](methyl)amino}acetic acid)