NP-MRD: Showing NP-Card for 6-Aminopenicillanic acid (NP0002695)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2020-11-23 19:38:09 UTC

Updated at

2021-08-19 23:59:15 UTC

NP-MRD ID

NP0002695

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-Aminopenicillanic acid

Provided By

NPAtlas

Description

6-Aminopenicillanic acid, also known as 6-APA or penicin, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. 6-Aminopenicillanic acid exists in all living organisms, ranging from bacteria to humans. 6-Aminopenicillanic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 6-Aminopenicillanic acid is found in Penicillium chrysogenum. It was first documented in 1990 (PMID: 1701026). Based on a literature review a significant number of articles have been published on 6-Aminopenicillanic acid (PMID: 17984079) (PMID: 14687482) (PMID: 1384868) (PMID: 24631718).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


     RDKit          2D

 26 27  0  0  0  0  0  0  0  0999 V2000
   -1.2957   -2.3920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9257   -0.9383    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4101   -0.7223    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4813   -1.4582    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.4105   -0.2806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6581    0.5521    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4909   -0.6955    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8254    1.7997    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1187    3.2708    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5778    0.9670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8661    0.5605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1194    2.0390    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0343    2.9976    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5265    2.5588    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1580   -2.7619    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0864   -2.2910    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6656   -3.8456    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6202   -1.4913    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3767    0.7773    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8945   -0.5064    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2863   -1.4985    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9057    1.3849    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9877   -0.5981    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9957   -2.1114    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3637    0.6463    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7798    4.0373    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  1
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 11  2  1  0
 10  5  1  0
  1 15  1  6
  1 16  1  0
  1 17  1  0
  3 18  1  1
  3 19  1  0
  3 20  1  0
  5 21  1  6
  6 22  1  6
  7 23  1  0
  7 24  1  0
 11 25  1  1
 14 26  1  0
M  END
> <DATABASE_ID>
NP0002695

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]1([H])N2C(=O)[C@@]([H])(N([H])[H])[C@@]2([H])SC1(C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1

> <INCHI_KEY>
NGHVIOIJCVXTGV-ALEPSDHESA-N

> <FORMULA>
C8H12N2O3S

> <MOLECULAR_WEIGHT>
216.257

> <EXACT_MASS>
216.05686295

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
20.698840293739135

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
-0.24

> <JCHEM_LOGP>
-2.8378366429456663

> <ALOGPS_LOGS>
-0.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.433548704443023

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.415152063079619

> <JCHEM_PKA_STRONGEST_BASIC>
7.403258608746982

> <JCHEM_POLAR_SURFACE_AREA>
83.63

> <JCHEM_REFRACTIVITY>
50.36210000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.55e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penin

> <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      -2.423  -0.307  -0.074  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.981  -0.485   0.342  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.984  -1.004   1.759  0.00  0.00           C+0
HETATM    4  S   UNK     0      -0.182  -1.698  -0.766  0.00  0.00           S+0
HETATM    5  C   UNK     0       1.045  -0.525  -1.412  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.462  -0.771  -0.934  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.529  -1.489   0.321  0.00  0.00           N+0
HETATM    8  C   UNK     0       2.407   0.679  -0.691  0.00  0.00           C+0
HETATM    9  O   UNK     0       3.197   1.627  -0.701  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.030   0.534  -0.432  0.00  0.00           N+0
HETATM   11  C   UNK     0      -0.243   0.774   0.155  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.955   1.807  -0.633  0.00  0.00           C+0
HETATM   13  O   UNK     0      -0.431   2.251  -1.688  0.00  0.00           O+0
HETATM   14  O   UNK     0      -2.207   2.331  -0.262  0.00  0.00           O+0
HETATM   15  H   UNK     0      -2.928   0.339   0.671  0.00  0.00           H+0
HETATM   16  H   UNK     0      -2.974  -1.276  -0.071  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.533   0.184  -1.063  0.00  0.00           H+0
HETATM   18  H   UNK     0      -1.152  -0.211   2.486  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.870  -1.694   1.835  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.106  -1.625   1.995  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.948  -0.248  -2.456  0.00  0.00           H+0
HETATM   22  H   UNK     0       3.163  -1.114  -1.712  0.00  0.00           H+0
HETATM   23  H   UNK     0       3.541  -1.406   0.641  0.00  0.00           H+0
HETATM   24  H   UNK     0       1.978  -0.942   1.021  0.00  0.00           H+0
HETATM   25  H   UNK     0      -0.138   1.230   1.188  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.196   3.038   0.478  0.00  0.00           H+0
CONECT    1    2   15   16   17                                             
CONECT    2    1    3    4   11                                             
CONECT    3    2   18   19   20                                             
CONECT    4    2    5                                                       
CONECT    5    4    6   10   21                                             
CONECT    6    5    7    8   22                                             
CONECT    7    6   23   24                                                  
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11    5                                                  
CONECT   11   10   12    2   25                                             
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   26                                                       
CONECT   15    1                                                            
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18    3                                                            
CONECT   19    3                                                            
CONECT   20    3                                                            
CONECT   21    5                                                            
CONECT   22    6                                                            
CONECT   23    7                                                            
CONECT   24    7                                                            
CONECT   25   11                                                            
CONECT   26   14                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(+)-6-Aminopenicillanic acid	ChEBI
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid	ChEBI
6-Aminopenicillamine acid	ChEBI
6-Aminopenicillanate	ChEBI
6-APA	ChEBI
6-Aps	ChEBI
6beta-Aminopenicillanic acid	ChEBI
Aminopenicillanic acid	ChEBI
Penicin	ChEBI
Penin	ChEBI
Phenacyl 6-aminopenicillinate	ChEBI
(+)-6-Aminopenicillanate	Generator
(2S,5R,6R)-6-Amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator
6b-Aminopenicillanate	Generator
6b-Aminopenicillanic acid	Generator
6beta-Aminopenicillanate	Generator
6Β-aminopenicillanate	Generator
6Β-aminopenicillanic acid	Generator
Aminopenicillanate	Generator
Phenacyl 6-aminopenicillinic acid	Generator
6-APA CPD	HMDB
Aminopenicillanic acid, potassium salt	HMDB
Aminopenicillanic acid, sodium salt	HMDB

Chemical Formula

C₈H₁₂N₂O₃S

Average Mass

216.2570 Da

Monoisotopic Mass

216.05686 Da

IUPAC Name

(2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

penin

CAS Registry Number

Not Available

SMILES

CC1(C)S[C@@H]2[C@H](N)C(=O)N2[C@H]1C(O)=O

InChI Identifier

InChI=1S/C8H12N2O3S/c1-8(2)4(7(12)13)10-5(11)3(9)6(10)14-8/h3-4,6H,9H2,1-2H3,(H,12,13)/t3-,4+,6-/m1/s1

InChI Key

NGHVIOIJCVXTGV-ALEPSDHESA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

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
Penicillium chrysogenum	NPAtlas	14448750

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	166.00 to 167.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	0.9 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	5.646 (est)	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	-0.24	ALOGPS
logP	-2.8	ChemAxon
logS	-0.59	ALOGPS
pKa (Strongest Acidic)	3.42	ChemAxon
pKa (Strongest Basic)	7.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	83.63 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	50.36 m³·mol⁻¹	ChemAxon
Polarizability	20.7 Å³	ChemAxon
Number of Rings	2	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

BMRB

HMDB ID

HMDB0060618

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10611

KEGG Compound ID

C02954

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

6-APA

METLIN ID

Not Available

PubChem Compound

11082

PDB ID

Not Available

ChEBI ID

16705

Good Scents ID

rw1300681

References

General References

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]
Zhao Y, Qiao H: Detection of specific IgE antibodies to major and minor antigenic determinants in sera of penicillin allergic patients. Chin Med J (Engl). 2003 Dec;116(12):1904-10. [PubMed:14687482 ]
Shimizu T, Souma S, Nagakura N, Masuzawa T, Iwamoto Y, Yanagihara Y: Epitope analysis of aztreonam by antiaztreonam monoclonal antibodies and possible consequences in beta-lactams hypersensitivity. Int Arch Allergy Immunol. 1992;98(4):392-7. doi: 10.1159/000236216. [PubMed:1384868 ]
Harle DG, Baldo BA: Identification of penicillin allergenic determinants that bind IgE antibodies in the sera of subjects with penicillin allergy. Mol Immunol. 1990 Nov;27(11):1063-71. doi: 10.1016/0161-5890(90)90094-g. [PubMed:1701026 ]
Ariza A, Barrionuevo E, Mayorga C, Montanez MI, Perez-Inestrosa E, Ruiz-Sanchez A, Rodriguez-Gueant RM, Fernandez TD, Gueant JL, Torres MJ, Blanca M: IgE to penicillins with different specificities can be identified by a multiepitope macromolecule: Bihaptenic penicillin structures and IgE specificities. J Immunol Methods. 2014 Apr;406:43-50. doi: 10.1016/j.jim.2014.03.001. Epub 2014 Mar 13. [PubMed:24631718 ]

Showing NP-Card for 6-Aminopenicillanic acid (NP0002695)

MOL for NP0002695 (6-Aminopenicillanic acid)

3D MOL for NP0002695 (6-Aminopenicillanic acid)

3D SDF for NP0002695 (6-Aminopenicillanic acid)

3D-SDF for NP0002695 (6-Aminopenicillanic acid)

PDB for NP0002695 (6-Aminopenicillanic acid)

3D PDB for NP0002695 (6-Aminopenicillanic acid)

SMILES for NP0002695 (6-Aminopenicillanic acid)

INCHI for NP0002695 (6-Aminopenicillanic acid)

Structure for NP0002695 (6-Aminopenicillanic acid)

3D Structure for NP0002695 (6-Aminopenicillanic acid)