NP-MRD: Showing NP-Card for L-2-amino-4-pentynoic acid (NP0021509)

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Record Information

Version

1.0

Created at

2021-01-06 06:47:42 UTC

Updated at

2021-07-15 17:36:32 UTC

NP-MRD ID

NP0021509

Secondary Accession Numbers

None

Natural Product Identification

Common Name

L-2-amino-4-pentynoic acid

Provided By

NPAtlas

Description

L-PROPARGYLGLYCINE is also known as (S)-propargylglycine or L-2-propynylglycine. L-2-amino-4-pentynoic acid is found in Streptomyces. It was first documented in 1971 (PMID: 4995438). Based on a literature review a significant number of articles have been published on L-PROPARGYLGLYCINE (PMID: 23772385) (PMID: 30867596) (PMID: 387077) (PMID: 3994731).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105163D          

 15 14  0  0  0  0            999 V2000
    3.0786    0.5759   -0.0101 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0058    0.0573    0.1914 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7191   -0.5852    0.4488 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3886    0.2035   -0.2147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3974    1.5359    0.3250 N   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6549   -0.5225    0.0447 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6178   -0.0138    0.6684 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7770   -1.8176   -0.4228 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0203    1.0282   -0.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6862   -1.6176    0.0172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4832   -0.6888    1.5129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1485    0.2742   -1.2845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0430    2.1756   -0.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4086    1.5650    1.3602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5573   -2.1700   -0.9508 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  1  9  1  0  0  0  0
  3 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  1  6  0  0  0
  5 13  1  0  0  0  0
  5 14  1  0  0  0  0
  8 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021509

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@@]([H])(N([H])[H])C([H])([H])C#C[H]

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c1-2-3-4(6)5(7)8/h1,4H,3,6H2,(H,7,8)/t4-/m0/s1

> <INCHI_KEY>
DGYHPLMPMRKMPD-BYPYZUCNSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.116

> <EXACT_MASS>
113.047678469

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.114585562777037

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-aminopent-4-ynoic acid

> <ALOGPS_LOGP>
-2.65

> <JCHEM_LOGP>
-2.6810064891526904

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.1471237036643136

> <JCHEM_PKA_STRONGEST_BASIC>
9.194075750060549

> <JCHEM_POLAR_SURFACE_AREA>
63.32000000000001

> <JCHEM_REFRACTIVITY>
28.0839

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-2-amino-4-pentynoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       3.079   0.576  -0.010  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.006   0.057   0.191  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.719  -0.585   0.449  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.389   0.204  -0.215  0.00  0.00           C+0
HETATM    5  N   UNK     0      -0.397   1.536   0.325  0.00  0.00           N+0
HETATM    6  C   UNK     0      -1.655  -0.523   0.045  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.618  -0.014   0.668  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.777  -1.818  -0.423  0.00  0.00           O+0
HETATM    9  H   UNK     0       4.020   1.028  -0.196  0.00  0.00           H+0
HETATM   10  H   UNK     0       0.686  -1.618   0.017  0.00  0.00           H+0
HETATM   11  H   UNK     0       0.483  -0.689   1.513  0.00  0.00           H+0
HETATM   12  H   UNK     0      -0.149   0.274  -1.285  0.00  0.00           H+0
HETATM   13  H   UNK     0      -1.043   2.176  -0.145  0.00  0.00           H+0
HETATM   14  H   UNK     0      -0.409   1.565   1.360  0.00  0.00           H+0
HETATM   15  H   UNK     0      -2.557  -2.170  -0.951  0.00  0.00           H+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10   11                                             
CONECT    4    3    5    6   12                                             
CONECT    5    4   13   14                                                  
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6   15                                                       
CONECT    9    1                                                            
CONECT   10    3                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
CONECT   14    5                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(S)-2-Amino-4-pentynoic acid	ChEBI
(S)-2-Propargylglycine	ChEBI
(S)-alpha-Propargylglycine	ChEBI
(S)-Propargylglycine	ChEBI
L-2-Propynylglycine	ChEBI
L-C-Propargylglycine	ChEBI
(S)-2-Amino-4-pentynoate	Generator
(S)-a-Propargylglycine	Generator
(S)-Α-propargylglycine	Generator
L-2-Amino-4-pentynoic acid	MeSH
Propargylglycine	MeSH
Propargylglycine hydrochloride	MeSH
Propargylglycine, (+-)-isomer	MeSH
Propargylglycine, (R)-isomer	MeSH
Propargylglycine, (S)-isomer	MeSH

Chemical Formula

C₅H₇NO₂

Average Mass

113.1160 Da

Monoisotopic Mass

113.04768 Da

IUPAC Name

(2S)-2-aminopent-4-ynoic acid

Traditional Name

(S)-2-amino-4-pentynoic acid

CAS Registry Number

Not Available

SMILES

N[C@@H](CC#C)C(O)=O

InChI Identifier

InChI=1S/C5H7NO2/c1-2-3-4(6)5(7)8/h1,4H,3,6H2,(H,7,8)/t4-/m0/s1

InChI Key

DGYHPLMPMRKMPD-BYPYZUCNSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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	NPAtlas	4995438

Chemical Taxonomy

Classification

Not classified

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	-2.6	ALOGPS
logP	-2.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.15	ChemAxon
pKa (Strongest Basic)	9.19	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	28.08 m³·mol⁻¹	ChemAxon
Polarizability	11.11 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

NPAtlas ID

NPA021207

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

147039

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

168091

PDB ID

Not Available

ChEBI ID

43797

Good Scents ID

Not Available

References

General References

Scannell JP, Pruess DL, Demny TC, Weiss F, Williams T: Antimetabolites produced by microorganisms. II. L-2-amino-4-pentynoic acid. J Antibiot (Tokyo). 1971 Apr;24(4):239-44. doi: 10.7164/antibiotics.24.239. [PubMed:4995438 ]
Mitra J, Bhattacharyya D: Irreversible inactivation of snake venom l-amino acid oxidase by covalent modification during catalysis of l-propargylglycine. FEBS Open Bio. 2013 Feb 4;3:135-43. doi: 10.1016/j.fob.2013.01.010. Print 2013. [PubMed:23772385 ]
Marchand JA, Neugebauer ME, Ing MC, Lin CI, Pelton JG, Chang MCY: Discovery of a pathway for terminal-alkyne amino acid biosynthesis. Nature. 2019 Mar;567(7748):420-424. doi: 10.1038/s41586-019-1020-y. Epub 2019 Mar 13. [PubMed:30867596 ]
Johnston M, Jankowski D, Marcotte P, Tanaka H, Esaki N, Soda K, Walsh C: Suicide inactivation of bacterial cystathionine gamma-synthase and methionine gamma-lyase during processing of L-propargylglycine. Biochemistry. 1979 Oct 16;18(21):4690-701. doi: 10.1021/bi00588a033. [PubMed:387077 ]
Sasaki K, Awata S, Kodama H: Effect of L-propargylglycine on metabolism of sulfur-containing amino acids in pregnant rats and their fetuses. Biochem Int. 1985 Feb;10(2):165-75. [PubMed:3994731 ]

Showing NP-Card for L-2-amino-4-pentynoic acid (NP0021509)

MOL for NP0021509 (L-2-amino-4-pentynoic acid)

3D MOL for NP0021509 (L-2-amino-4-pentynoic acid)

3D SDF for NP0021509 (L-2-amino-4-pentynoic acid)

3D-SDF for NP0021509 (L-2-amino-4-pentynoic acid)

PDB for NP0021509 (L-2-amino-4-pentynoic acid)

3D PDB for NP0021509 (L-2-amino-4-pentynoic acid)

SMILES for NP0021509 (L-2-amino-4-pentynoic acid)

INCHI for NP0021509 (L-2-amino-4-pentynoic acid)

Structure for NP0021509 (L-2-amino-4-pentynoic acid)

3D Structure for NP0021509 (L-2-amino-4-pentynoic acid)