NP-MRD: Showing NP-Card for (5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid (NP0220441)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on NP-MRD.

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-05 21:45:01 UTC

Updated at

2022-09-05 21:45:01 UTC

NP-MRD ID

NP0220441

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

Description

PS-5, also known as antibiotic PS 5, belongs to the class of organic compounds known as carbapenems. These are beta-lactam derivatives in which the beta-lactam ring shares the nitrogen atom with a pyrrole-2-carboxylic acid. (5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid is found in Apis cerana. (5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid was first documented in 2021 (PMID: 35480178). Based on a literature review very few articles have been published on PS-5 (PMID: 35978752).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052223452D          

 20 21  0  0  1  0            999 V2000
   -0.4319   -0.9460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -1.1595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9483   -0.5762    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9483    0.2488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649    0.8322    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733    0.2488    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579    0.5038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8129    1.2884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6198    1.4599    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2608    1.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0428   -0.1637    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8678   -0.1637    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.2803    0.5508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1053    0.5508    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5178    1.2653    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3428    1.2653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7553    1.9797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7553    0.5508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5579   -0.8311    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7733   -0.5762    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  7 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  4  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 11 19  1  0  0  0  0
 19 20  1  0  0  0  0
  3 20  1  0  0  0  0
 20  6  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0220441

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H]1[C@H]2CC(SCCN=C(C)O)=C(N2C1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H18N2O4S/c1-3-8-9-6-10(20-5-4-14-7(2)16)11(13(18)19)15(9)12(8)17/h8-9H,3-6H2,1-2H3,(H,14,16)(H,18,19)/t8-,9-/m1/s1

> <INCHI_KEY>
MHSNTZYKSLYGOM-RKDXNWHRSA-N

> <FORMULA>
C13H18N2O4S

> <MOLECULAR_WEIGHT>
298.36

> <EXACT_MASS>
298.098728242

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
31.51474951848741

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,6R)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <JCHEM_LOGP>
-1.1894452549978782

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.382190741719789

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.680672331886239

> <JCHEM_PKA_STRONGEST_BASIC>
6.216332083386885

> <JCHEM_POLAR_SURFACE_AREA>
90.2

> <JCHEM_REFRACTIVITY>
77.08390000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5R,6R)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.806  -1.766   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.681  -2.164   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.770  -1.076   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.770   0.464   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.681   1.553   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       3.310   0.464   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.775   0.940   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.251   2.405   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.757   2.725   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.220   3.549   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.680  -0.306   0.000  0.00  0.00           C+0
HETATM   12  S   UNK     0       7.220  -0.306   0.000  0.00  0.00           S+0
HETATM   13  C   UNK     0       7.990   1.028   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.530   1.028   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      10.300   2.362   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      11.840   2.362   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.610   3.695   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      12.610   1.028   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.775  -1.551   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.310  -1.076   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   20                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   20                                                  
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   11   20                                                       
CONECT   20   19    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   20    0   42    0
END

View in JSmol

Synonyms

Value	Source
Antibiotic PS 5	Kegg
PS 5	MeSH
PS 5, Sodium salt, (5R-cis)-isomer	MeSH
3-(2-Acetamidoethyl)thio-6-ethyl-7-oxo-1-azabicyclo(3.2.0)hept-2-ene-2-carboxylic acid	MeSH

Chemical Formula

C₁₃H₁₈N₂O₄S

Average Mass

298.3600 Da

Monoisotopic Mass

298.09873 Da

IUPAC Name

(5R,6R)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

Traditional Name

(5R,6R)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC[C@@H]1[C@H]2CC(SCCN=C(C)O)=C(N2C1=O)C(O)=O

InChI Identifier

InChI=1S/C13H18N2O4S/c1-3-8-9-6-10(20-5-4-14-7(2)16)11(13(18)19)15(9)12(8)17/h8-9H,3-6H2,1-2H3,(H,14,16)(H,18,19)/t8-,9-/m1/s1

InChI Key

MHSNTZYKSLYGOM-RKDXNWHRSA-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
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as carbapenems. These are beta-lactam derivatives in which the beta-lactam ring shares the nitrogen atom with a pyrrole-2-carboxylic acid.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactams

Sub Class

Beta lactams

Direct Parent

Carbapenems

Alternative Parents

Substituents

Carbapenem
Alpha-amino acid or derivatives
Pyrroline carboxylic acid
Pyrroline carboxylic acid or derivatives
Azepine
Vinylogous thioester
Acetamide
Tertiary carboxylic acid amide
Pyrroline
Thioenolether
Secondary carboxylic acid amide
Azetidine
Carboxamide group
Azacycle
Sulfenyl compound
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organosulfur compound
Organic oxide
Carbonyl group
Organopnictogen compound
Hydrocarbon derivative
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

carbapenems (CHEBI:81037 )

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	-1.2	ChemAxon
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	6.22	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	90.2 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	77.08 m³·mol⁻¹	ChemAxon
Polarizability	31.51 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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

170200

KEGG Compound ID

C17370

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

PlayStation 5

METLIN ID

Not Available

PubChem Compound

196445

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Turnbull ZA, Tangel VE, Goldstein PA: Predictive Value of Emergency Designation on Outcomes of Moribund Patients. Cureus. 2022 Jul 15;14(7):e26875. doi: 10.7759/cureus.26875. eCollection 2022 Jul. [PubMed:35978752 ]
Dastbaz Z, Dana SN, Ashrafizadeh SN: Preparation of a stabilized aqueous polystyrene suspension via phase inversion. RSC Adv. 2021 May 13;11(29):17547-17557. doi: 10.1039/d1ra02292j. eCollection 2021 May 13. [PubMed:35480178 ]
LOTUS database [Link]

Showing NP-Card for (5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid (NP0220441)

MOL for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D MOL for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D SDF for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D-SDF for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

PDB for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D PDB for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

SMILES for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

INCHI for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

Structure for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)

3D Structure for NP0220441 ((5r,6r)-6-ethyl-3-({2-[(1-hydroxyethylidene)amino]ethyl}sulfanyl)-7-oxo-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid)