NP-MRD: Showing NP-Card for Antibiotic SF 2103A (NP0062139)

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Record Information

Version

2.0

Created at

2022-04-28 06:48:19 UTC

Updated at

2022-04-28 06:48:19 UTC

NP-MRD ID

NP0062139

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Antibiotic SF 2103A

Description

Pluracidomycin, also known as SF 2103 a, 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. Antibiotic SF 2103A is found in Streptomyces pluracidomyceticus nov. sp. (PA-41746). Antibiotic SF 2103A was first documented in 1985 (PMID: 3997673). Based on a literature review very few articles have been published on Pluracidomycin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 33 34  0  0  0  0  0  0  0  0999 V2000
    3.3180   -0.7049    1.3226 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1604   -0.1382    0.4697 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4965    1.1440    0.0301 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7534    1.2741   -1.5955 S   0  0  2  0  0  6  0  0  0  0  0  0
    4.1815    1.6956   -1.8392 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8933    2.4224   -2.1057 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3677   -0.1312   -2.4263 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0174   -0.0092    1.4168 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3522   -1.3077    1.6711 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6196   -2.4070    2.2481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8115   -0.8885    0.9888 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0711   -0.7172    0.3027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2220   -1.5782    0.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3128   -1.4272   -0.0726 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1215   -2.6410    1.3934 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0066    0.3198   -0.5047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2245    0.9869   -1.5641 S   0  0  2  0  0  6  0  0  0  0  0  0
   -4.1050   -0.0132   -2.2049 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5542    1.7654   -2.6939 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1706    2.0938   -0.7358 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6242    0.8910   -0.3640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2786    0.4865    1.0097 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2761   -0.2611    2.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1279   -1.7926    1.4367 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2853   -0.5665    0.8066 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0533   -0.8480   -0.3458 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2321   -0.4863   -2.7975 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4013    0.4788    2.3641 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8839   -3.5643    1.1008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7079    2.4351    0.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5951    1.9674   -0.5681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0516    0.3883   -1.1666 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7950    1.1333    1.7505 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  4  3  1  1
  4  7  1  0
  4  5  2  0
  4  6  2  0
  2  8  1  0
  8 22  1  0
 22 21  1  0
 21 16  1  0
 16 12  2  0
 12 11  1  0
 11  9  1  0
  9 10  2  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
 16 17  1  0
 17 20  1  1
 17 18  2  0
 17 19  2  0
  9  8  1  0
 11 22  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  6
  7 27  1  0
  8 28  1  1
 22 33  1  1
 21 31  1  0
 21 32  1  0
 15 29  1  0
 20 30  1  0
M  END


  Mrv1652304282208482D          

 22 23  0  0  1  0            999 V2000
    0.6773   -0.9323    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6773   -0.1073    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469   -0.5198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620   -1.1872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7719   -0.5198    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.5969   -0.5198    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7719    0.3052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7719   -1.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    0.9323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    1.1038    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649    1.5454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.1073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310    0.4761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477   -0.9323    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7310   -1.5156    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5175   -2.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5279   -1.3021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1113   -1.8855    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6946   -2.4688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6946   -1.3021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5279   -2.4688    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
  3 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
  1 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  6  0  0  0
 16 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  2  0  0  0  0
 19 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062139

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C9H11NO10S2/c1-3(20-22(17,18)19)6-4-2-5(21(14,15)16)7(9(12)13)10(4)8(6)11/h3-4,6H,2H2,1H3,(H,12,13)(H,14,15,16)(H,17,18,19)/t3-,4+,6-/m0/s1

> <INCHI_KEY>
KSUVJVOKUIADCL-RPDRRWSUSA-N

> <FORMULA>
C9H11NO10S2

> <MOLECULAR_WEIGHT>
357.3

> <EXACT_MASS>
356.982437906

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
33

> <JCHEM_AVERAGE_POLARIZABILITY>
29.40832644157925

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(5R,6R)-7-oxo-3-sulfo-6-[(1S)-1-(sulfooxy)ethyl]-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <ALOGPS_LOGP>
-2.15

> <JCHEM_LOGP>
-2.3504581026666664

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
-1.3388548336626336

> <JCHEM_PKA_STRONGEST_ACIDIC>
-2.23994588745546

> <JCHEM_PKA_STRONGEST_BASIC>
-9.723907715789146

> <JCHEM_POLAR_SURFACE_AREA>
175.58

> <JCHEM_REFRACTIVITY>
68.4133

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.73e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R,6R)-7-oxo-3-sulfo-6-[(1S)-1-(sulfooxy)ethyl]-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       1.264  -1.740   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.264  -0.200   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.729   0.276   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.634  -0.970   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.729  -2.216   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       5.174  -0.970   0.000  0.00  0.00           S+0
HETATM    7  O   UNK     0       6.714  -0.970   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.174   0.570   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       5.174  -2.510   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.205   1.740   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.711   2.060   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       2.174   2.885   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -0.276  -0.200   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.365   0.889   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -0.276  -1.740   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.365  -2.829   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.966  -4.317   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.852  -2.431   0.000  0.00  0.00           O+0
HETATM   19  S   UNK     0      -3.941  -3.520   0.000  0.00  0.00           S+0
HETATM   20  O   UNK     0      -5.030  -4.609   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -5.030  -2.431   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -2.852  -4.609   0.000  0.00  0.00           O+0
CONECT    1    2    5   15                                                  
CONECT    2    1    3   13                                                  
CONECT    3    2    4   10                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    1                                                       
CONECT    6    4    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    3   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    2   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    1   16                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   21   22                                             
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   19                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   46    0
END

View in JSmol

Synonyms

Value	Source
SF 2103 a	MeSH
Pluracidomycin a	MeSH

Chemical Formula

C₉H₁₁NO₁₀S₂

Average Mass

357.3000 Da

Monoisotopic Mass

356.98244 Da

IUPAC Name

(5R,6R)-7-oxo-3-sulfo-6-[(1S)-1-(sulfooxy)ethyl]-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

Traditional Name

(5R,6R)-7-oxo-3-sulfo-6-[(1S)-1-(sulfooxy)ethyl]-1-azabicyclo[3.2.0]hept-2-ene-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H11NO10S2/c1-3(20-22(17,18)19)6-4-2-5(21(14,15)16)7(9(12)13)10(4)8(6)11/h3-4,6H,2H2,1H3,(H,12,13)(H,14,15,16)(H,17,18,19)/t3-,4+,6-/m0/s1

InChI Key

KSUVJVOKUIADCL-RPDRRWSUSA-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 pluracidomyceticus nov. sp. (PA-41746)	Bacteria	KNApSAcK

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
Sulfuric acid monoester
Sulfate-ester
Alkyl sulfate
Sulfuric acid ester
Sulfonyl
Organosulfonic acid
Organosulfonic acid or derivatives
Organic sulfonic acid or derivatives
Pyrroline
Tertiary carboxylic acid amide
Organic sulfuric acid or derivatives
Azetidine
Carboxamide group
Azacycle
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organosulfur compound
Carbonyl group
Organic oxide
Organic nitrogen compound
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

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	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	-2.2	ChemAxon
pKa (Strongest Basic)	-9.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	175.58 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	68.41 m³·mol⁻¹	ChemAxon
Polarizability	29.41 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

C00018422

Chemspider ID

4589451

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5487610

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Tsuji N, Kobayashi M, Terui Y, Matsumoto K, Takahashi Y, Kondo E: Pluracidomycin A2, a new carbapenem bearing a sulfinic acid, and other minor pluracidomycins. J Antibiot (Tokyo). 1985 Feb;38(2):270-4. doi: 10.7164/antibiotics.38.270. [PubMed:3997673 ]

Showing NP-Card for Antibiotic SF 2103A (NP0062139)

MOL for NP0062139 (Antibiotic SF 2103A)

3D MOL for NP0062139 (Antibiotic SF 2103A)

3D SDF for NP0062139 (Antibiotic SF 2103A)

3D-SDF for NP0062139 (Antibiotic SF 2103A)

PDB for NP0062139 (Antibiotic SF 2103A)

3D PDB for NP0062139 (Antibiotic SF 2103A)

SMILES for NP0062139 (Antibiotic SF 2103A)

INCHI for NP0062139 (Antibiotic SF 2103A)

Structure for NP0062139 (Antibiotic SF 2103A)

3D Structure for NP0062139 (Antibiotic SF 2103A)