NP-MRD: Showing NP-Card for (2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid (NP0329398)

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Record Information

Version

2.0

Created at

2022-09-12 13:44:28 UTC

Updated at

2022-09-12 13:44:28 UTC

NP-MRD ID

NP0329398

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid

Description

(2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid 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. (2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid is found in Pseudomonas syringae. Based on a literature review very few articles have been published on (2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309122215442D          

 16 15  0  0  1  0            999 V2000
    1.2375    0.7145    0.0000 C   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 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -2.8579    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750   -2.8579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -4.2868    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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  4  0  0  0
  6  5  1  1  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0329398

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(O)=NC[C@@](O)(CO)CC[C@H](N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H18N2O5/c1-6(13)11-4-9(16,5-12)3-2-7(10)8(14)15/h7,12,16H,2-5,10H2,1H3,(H,11,13)(H,14,15)/t7-,9+/m0/s1

> <INCHI_KEY>
YSIYXKLKKBSLKF-IONNQARKSA-N

> <FORMULA>
C9H18N2O5

> <MOLECULAR_WEIGHT>
234.252

> <EXACT_MASS>
234.121571688

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.386647766638482

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid

> <JCHEM_LOGP>
-4.2686486301383

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.121200826399502

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.2344557854897538

> <JCHEM_PKA_STRONGEST_BASIC>
9.223656236036593

> <JCHEM_POLAR_SURFACE_AREA>
136.37

> <JCHEM_REFRACTIVITY>
55.318400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.334  -3.437   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334  -1.897   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667  -2.667   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.770  -4.001   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.310  -4.001   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.080  -5.335   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.620  -5.335   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.310  -6.668   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.080  -8.002   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.770  -6.668   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   10                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

View in JSmol

Synonyms

Value	Source
(2S,5R)-2-Amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoate	Generator

Chemical Formula

C₉H₁₈N₂O₅

Average Mass

234.2520 Da

Monoisotopic Mass

234.12157 Da

IUPAC Name

(2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid

Traditional Name

(2S,5R)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid

CAS Registry Number

Not Available

SMILES

CC(O)=NC[C@@](O)(CO)CC[C@H](N)C(O)=O

InChI Identifier

InChI=1S/C9H18N2O5/c1-6(13)11-4-9(16,5-12)3-2-7(10)8(14)15/h7,12,16H,2-5,10H2,1H3,(H,11,13)(H,14,15)/t7-,9+/m0/s1

InChI Key

YSIYXKLKKBSLKF-IONNQARKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Pseudomonas syringae	LOTUS Database	35616633

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

Substituents

L-alpha-amino acid
Medium-chain hydroxy acid
Medium-chain fatty acid
Amino fatty acid
Branched fatty acid
Hydroxy fatty acid
Fatty acyl
Fatty acid
Tertiary alcohol
1,2-diol
Amino acid
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Alcohol
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Primary alcohol
Primary amine
Organic oxygen compound
Organopnictogen 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	-4.3	ChemAxon
pKa (Strongest Acidic)	2.23	ChemAxon
pKa (Strongest Basic)	9.22	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	55.32 m³·mol⁻¹	ChemAxon
Polarizability	23.39 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

75253960

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162885621

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid (NP0329398)

MOL for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

3D MOL for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

3D SDF for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

3D-SDF for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

PDB for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

3D PDB for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

SMILES for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

INCHI for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

Structure for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)

3D Structure for NP0329398 ((2s,5r)-2-amino-5,6-dihydroxy-5-{[(1-hydroxyethylidene)amino]methyl}hexanoic acid)