NP-MRD: Showing NP-Card for 4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid (NP0304984)

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Record Information

Version

2.0

Created at

2022-09-10 20:27:14 UTC

Updated at

2022-09-10 20:27:14 UTC

NP-MRD ID

NP0304984

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid

Description

Gaburedin D belongs to the class of organic compounds known as gamma amino acids and derivatives. These are amino acids having a (-NH2) group attached to the gamma carbon atom. 4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid is found in Streptomyces venezuelae. Based on a literature review very few articles have been published on Gaburedin D.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 36  0  0  0  0  0  0  0  0999 V2000
   -3.0769    1.5548   -1.2239 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1012    0.3991   -1.0896 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7082    0.9222   -1.3451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2232   -0.2996    0.2187 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3252   -1.3986    0.3562 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0857   -1.3515    0.4062 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7869   -1.9515   -0.6175 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7235   -0.7744    1.3648 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1709   -0.7246    1.4137 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7327    0.0455    0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2545    0.0863    0.3654 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8358    0.8252   -0.7817 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5657    0.5493   -1.9902 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7168    1.8701   -0.5034 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6569   -0.6730    0.5480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6694   -1.1225    1.8875 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4789    0.4516    0.5395 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0559    1.2614   -1.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6429    2.2170   -2.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1376    2.1835   -0.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3821   -0.3163   -1.9198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8137    1.8837   -1.9003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1685    0.1688   -1.9515 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2557    1.1332   -0.3755 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9397    0.4392    1.0339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7539   -2.3644    0.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4005   -2.1427   -1.5287 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5897   -1.7454    1.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5194   -0.2339    2.3404 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3308    1.0702    0.2900 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5180   -0.3964   -0.7232 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5762    0.5695    1.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6647   -0.9641    0.3159 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1833    2.0233    0.3638 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0512   -1.4910   -0.0652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9283   -2.0564    1.9446 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2854    0.3526    1.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 14  1  0
 12 13  2  0
  4 15  1  0
 15 16  1  0
 15 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  2 21  1  0
  3 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  1
  5 26  1  0
  7 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 14 34  1  0
 15 35  1  0
 16 36  1  0
 17 37  1  0
M  END


  Mrv1652309102222272D          

 17 16  0  0  1  0            999 V2000
   -3.7638    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0493    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0493   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6204    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   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
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3349    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204    2.3645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0493    2.3645    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  1  0  0  0  0
  4  5  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  4  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
  4 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0304984

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H20N2O5/c1-6(2)8(9(15)16)12-10(17)11-5-3-4-7(13)14/h6,8-9,15-16H,3-5H2,1-2H3,(H,13,14)(H2,11,12,17)/t8-/m0/s1

> <INCHI_KEY>
LONZXPSSYXJXOI-QMMMGPOBSA-N

> <FORMULA>
C10H20N2O5

> <MOLECULAR_WEIGHT>
248.279

> <EXACT_MASS>
248.137221752

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.45832948553585

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-{N-[(2S)-1,1-dihydroxy-3-methylbutan-2-yl]-(C-hydroxycarbonimidoyl)amino}butanoic acid

> <JCHEM_LOGP>
-1.377948065050758

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.6655106669871045

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.8147611402819885

> <JCHEM_PKA_STRONGEST_BASIC>
15.039671130327223

> <JCHEM_POLAR_SURFACE_AREA>
122.38000000000001

> <JCHEM_REFRACTIVITY>
59.73329999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
4-{N-[(2S)-1,1-dihydroxy-3-methylbutan-2-yl]-(C-hydroxycarbonimidoyl)amino}butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -7.026   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.692   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.692  -0.206   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.358   2.104   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -3.025   1.334   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.691   3.644   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      -0.357   1.334   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.358   3.644   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -3.025   4.414   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -5.692   4.414   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    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    4   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

C₁₀H₂₀N₂O₅

Average Mass

248.2790 Da

Monoisotopic Mass

248.13722 Da

IUPAC Name

4-{N-[(2S)-1,1-dihydroxy-3-methylbutan-2-yl]-(C-hydroxycarbonimidoyl)amino}butanoic acid

Traditional Name

4-{N-[(2S)-1,1-dihydroxy-3-methylbutan-2-yl]-(C-hydroxycarbonimidoyl)amino}butanoic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@H](NC(O)=NCCCC(O)=O)C(O)O

InChI Identifier

InChI=1S/C10H20N2O5/c1-6(2)8(9(15)16)12-10(17)11-5-3-4-7(13)14/h6,8-9,15-16H,3-5H2,1-2H3,(H,13,14)(H2,11,12,17)/t8-/m0/s1

InChI Key

LONZXPSSYXJXOI-QMMMGPOBSA-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 venezuelae	LOTUS Database	35616633

Chemical Taxonomy

Description

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

Gamma amino acids and derivatives

Alternative Parents

Substituents

Gamma amino acid or derivatives
Hydroxy fatty acid
Branched fatty acid
Fatty acyl
Fatty acid
Isourea
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Monocarboxylic acid or derivatives
Carboxylic acid
Carboximidic acid derivative
Carbonyl hydrate
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
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	-1.4	ChemAxon
pKa (Strongest Acidic)	-2.8	ChemAxon
pKa (Strongest Basic)	15.04	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	122.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	59.73 m³·mol⁻¹	ChemAxon
Polarizability	25.46 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

146684678

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid (NP0304984)

MOL for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

3D MOL for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

3D SDF for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

3D-SDF for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

PDB for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

3D PDB for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

SMILES for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

INCHI for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

Structure for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)

3D Structure for NP0304984 (4-{n-[(2s)-1,1-dihydroxy-3-methylbutan-2-yl]-(c-hydroxycarbonimidoyl)amino}butanoic acid)