NP-MRD: Showing NP-Card for (2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid (NP0141550)

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Record Information

Version

2.0

Created at

2022-09-01 19:53:47 UTC

Updated at

2022-09-01 19:53:47 UTC

NP-MRD ID

NP0141550

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid

Description

(2S)-2-amino-5-[(4-hydroxy-5-methyl-2,5-dihydro-1H-imidazol-2-ylidene)amino]pentanoic acid belongs to the class of organic compounds known as arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. Based on a literature review very few articles have been published on (2S)-2-amino-5-[(4-hydroxy-5-methyl-2,5-dihydro-1H-imidazol-2-ylidene)amino]pentanoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 32  0  0  0  0  0  0  0  0999 V2000
    4.7121   -0.4586    1.2297 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1205   -0.0038   -0.0849 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7476   -0.3569   -0.2337 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0178    0.8431   -0.4294 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7337    0.9999   -0.6096 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1487   -0.1265   -0.6296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4784    0.2758   -0.0101 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4398   -0.8679   -0.0060 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7644   -0.5091    0.6135 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6082   -1.7172    0.5580 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4480    0.5833   -0.0997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0060    1.7520   -0.1600 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6529    0.3266   -0.7498 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9688    1.8861   -0.3935 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1460    1.4616   -0.2048 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3310    2.2228   -0.1147 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1193   -0.0452    2.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7405   -0.0532    1.2774 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7861   -1.5460    1.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6984   -0.4647   -0.9157 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2944   -1.3179   -0.2118 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2785   -1.0145   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3486   -0.4144   -1.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3550    0.6581    1.0207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8462    1.1532   -0.6189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9879   -1.7041    0.5588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6062   -1.2008   -1.0671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5881   -0.2551    1.6892 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2249   -1.6423   -0.2850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0028   -2.5627    0.4361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4825    0.8963   -0.5970 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2941    3.2018    0.1827 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  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 13  1  0
 11 12  2  0
  4 14  1  0
 14 15  2  0
 15 16  1  0
 15  2  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  6
  3 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  1
 10 29  1  0
 10 30  1  0
 13 31  1  0
 16 32  1  0
M  END


  Mrv1652309012221532D          

 16 16  0  0  1  0            999 V2000
   -1.2382    4.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7231    3.4814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4681    2.6968    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1356    2.2119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1356    1.3869    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4211    0.9744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7066    1.3869    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0078    0.9744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7223    1.3869    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7223    2.2119    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4368    0.9744    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1512    1.3869    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4368    0.1494    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8030    2.6968    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5481    3.4814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0330    4.1488    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  2  0  0  0  0
  5  6  1  4  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  4 14  1  0  0  0  0
 14 15  2  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0141550

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1NC(=NCCC[C@H](N)C(O)=O)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16N4O3/c1-5-7(14)13-9(12-5)11-4-2-3-6(10)8(15)16/h5-6H,2-4,10H2,1H3,(H,15,16)(H2,11,12,13,14)/t5?,6-/m0/s1

> <INCHI_KEY>
KGQMQNPFMOBJCY-GDVGLLTNSA-N

> <FORMULA>
C9H16N4O3

> <MOLECULAR_WEIGHT>
228.252

> <EXACT_MASS>
228.122240391

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.814629957789652

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-5-[(4-hydroxy-5-methyl-2,5-dihydro-1H-imidazol-2-ylidene)amino]pentanoic acid

> <ALOGPS_LOGP>
-3.24

> <JCHEM_LOGP>
-4.5372949888405225

> <ALOGPS_LOGS>
-2.46

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
1.9931718110884415

> <JCHEM_PKA_STRONGEST_ACIDIC>
-4.605096245040557

> <JCHEM_PKA_STRONGEST_BASIC>
14.955858849738101

> <JCHEM_POLAR_SURFACE_AREA>
120.3

> <JCHEM_REFRACTIVITY>
56.305200000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.91e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 01-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.311   7.745   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.216   6.499   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -2.741   5.034   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -3.986   4.129   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -3.986   2.589   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.653   1.819   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.319   2.589   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.015   1.819   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.348   2.589   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.348   4.129   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       2.682   1.819   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.016   2.589   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.682   0.279   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      -5.232   5.034   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -4.756   6.499   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.662   7.745   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   14                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    4   15                                                       
CONECT   15   14    2   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Value	Source
(2S)-2-Amino-5-[(4-hydroxy-5-methyl-2,5-dihydro-1H-imidazol-2-ylidene)amino]pentanoate	Generator

Chemical Formula

C₉H₁₆N₄O₃

Average Mass

228.2520 Da

Monoisotopic Mass

228.12224 Da

IUPAC Name

(2S)-2-amino-5-[(4-hydroxy-5-methyl-2,5-dihydro-1H-imidazol-2-ylidene)amino]pentanoic acid

Traditional Name

(2S)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid

CAS Registry Number

Not Available

SMILES

CC1NC(=NCCC[C@H](N)C(O)=O)N=C1O

InChI Identifier

InChI=1S/C9H16N4O3/c1-5-7(14)13-9(12-5)11-4-2-3-6(10)8(15)16/h5-6H,2-4,10H2,1H3,(H,15,16)(H2,11,12,13,14)/t5?,6-/m0/s1

InChI Key

KGQMQNPFMOBJCY-GDVGLLTNSA-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 arginine and derivatives. Arginine and derivatives are compounds containing arginine or a derivative thereof resulting from reaction of arginine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Arginine and derivatives

Alternative Parents

Substituents

Arginine or derivatives
Alpha-amino acid
L-alpha-amino acid
Imidazolyl carboxylic acid derivative
Heterocyclic fatty acid
Imidazolinone
Fatty acid
Fatty acyl
2-imidazoline
Guanidine
Amino acid
Azacycle
Carboxylic acid
Monocarboxylic acid or derivatives
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Organoheterocyclic compound
Amine
Primary aliphatic amine
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Primary amine
Carbonyl group
Organic nitrogen compound
Hydrocarbon derivative
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-3.2	ALOGPS
logP	-4.5	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	-4.6	ChemAxon
pKa (Strongest Basic)	14.96	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	120.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	56.31 m³·mol⁻¹	ChemAxon
Polarizability	23.81 Å³	ChemAxon
Number of Rings	1	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

113261

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

127667

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid (NP0141550)

MOL for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

3D MOL for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

3D SDF for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

3D-SDF for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

PDB for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

3D PDB for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

SMILES for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

INCHI for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

Structure for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)

3D Structure for NP0141550 ((2s)-2-amino-5-[(4-hydroxy-5-methyl-1,5-dihydroimidazol-2-ylidene)amino]pentanoic acid)