NP-MRD: Showing NP-Card for (2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid (NP0264691)

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Record Information

Version

2.0

Created at

2022-09-08 08:20:48 UTC

Updated at

2022-09-08 08:20:48 UTC

NP-MRD ID

NP0264691

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

6-Formamidopenicillanic acid, also known as 6beta-formylaminopenicillanate, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. (2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid is found in Sarocladium strictum. (2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid was first documented in 1979 (PMID: 41925). Based on a literature review very few articles have been published on 6-formamidopenicillanic acid (PMID: 6166603).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
   -2.9007   -0.9916    0.3518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6306   -0.2439    0.5515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7391    0.5866    1.8046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1882   -1.3769    0.6662 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.8070   -0.6003   -0.6468 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1207   -0.0475   -0.2135 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4135   -0.0363    1.1798 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6478    0.1408    1.5438 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6751    0.3171    0.6189 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5369    1.2445   -0.6532 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9995    2.3717   -0.9409 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1878    0.7292   -0.6338 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2327    0.6155   -0.6121 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7292    0.1609   -1.9048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9404   -0.0280   -2.1670 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8240   -0.0833   -2.9204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8324   -1.8558   -0.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2005   -1.4102    1.3533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6810   -0.2825    0.0352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7107    0.8582    2.1694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3124    1.5086    1.5712 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2790   -0.0205    2.5759 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8106   -1.1116   -1.6060 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9473   -0.3511   -0.8656 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9336    0.1592    2.5881 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8708   -0.4995    0.0228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6608    1.6222   -0.4239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0889    0.6033   -3.1181 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  6 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 14 16  1  0
 14 15  2  0
 13  2  1  0
 12  5  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  3 20  1  0
  3 21  1  0
  3 22  1  0
  5 23  1  6
  6 24  1  6
  8 25  1  0
  9 26  1  0
 13 27  1  1
 16 28  1  0
M  END


  Mrv1652309082210202D          

 16 17  0  0  1  0            999 V2000
    2.5600    0.7927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9469    1.3448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5600    1.8968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    0.6773    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    0.9323    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1477    0.9323    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7310    0.3489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5279    0.5624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1113   -0.0209    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1477    1.7573    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7310    2.3406    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    1.7573    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4620    2.0122    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7169    2.7968    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1649    3.4099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    2.9684    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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  0  0  0
  7  8  2  0  0  0  0
  8  9  1  4  0  0  0
  6 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  6  0  0  0
 12 13  1  0  0  0  0
  2 13  1  0  0  0  0
 13 14  1  1  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0264691

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1(C)S[C@@H]2[C@H](N=CO)C(=O)N2[C@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H12N2O4S/c1-9(2)5(8(14)15)11-6(13)4(10-3-12)7(11)16-9/h3-5,7H,1-2H3,(H,10,12)(H,14,15)/t4-,5+,7-/m1/s1

> <INCHI_KEY>
MDQGTDMBVJCTBN-JCGDXUMPSA-N

> <FORMULA>
C9H12N2O4S

> <MOLECULAR_WEIGHT>
244.27

> <EXACT_MASS>
244.051778048

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
22.823006176601034

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
0.017243552333333315

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.237891103580993

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4036034959134227

> <JCHEM_PKA_STRONGEST_BASIC>
1.0453207345333932

> <JCHEM_POLAR_SURFACE_AREA>
90.2

> <JCHEM_REFRACTIVITY>
55.83710000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       4.779   1.480   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.634   2.510   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.779   3.541   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       2.729   1.264   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0       1.264   1.740   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.276   1.740   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.365   0.651   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.852   1.050   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.941  -0.039   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -0.276   3.280   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.365   4.369   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       1.264   3.280   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.729   3.756   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.205   5.221   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.174   6.365   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.711   5.541   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   13                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    6   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    5   13                                                  
CONECT   13   12    2   14                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
(2S,5R,6R)-6-Formamido-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid	ChEBI
6-Formamido-2,2-dimethylpenam-3alpha-carboxylic acid	ChEBI
6beta-Formylaminopenicillanic acid	ChEBI
(2S,5R,6R)-6-Formamido-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator
6-Formamido-2,2-dimethylpenam-3a-carboxylate	Generator
6-Formamido-2,2-dimethylpenam-3a-carboxylic acid	Generator
6-Formamido-2,2-dimethylpenam-3alpha-carboxylate	Generator
6-Formamido-2,2-dimethylpenam-3α-carboxylate	Generator
6-Formamido-2,2-dimethylpenam-3α-carboxylic acid	Generator
6b-Formylaminopenicillanate	Generator
6b-Formylaminopenicillanic acid	Generator
6beta-Formylaminopenicillanate	Generator
6Β-formylaminopenicillanate	Generator
6Β-formylaminopenicillanic acid	Generator
6-Formamidopenicillanate	Generator

Chemical Formula

C₉H₁₂N₂O₄S

Average Mass

244.2700 Da

Monoisotopic Mass

244.05178 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C9H12N2O4S/c1-9(2)5(8(14)15)11-6(13)4(10-3-12)7(11)16-9/h3-5,7H,1-2H3,(H,10,12)(H,14,15)/t4-,5+,7-/m1/s1

InChI Key

MDQGTDMBVJCTBN-JCGDXUMPSA-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
Acremonium strictum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
Penam
Beta-lactam
Tertiary carboxylic acid amide
Thiazolidine
Azetidine
Carboxamide group
Lactam
Azacycle
Organoheterocyclic compound
Dialkylthioether
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Thioether
Hemithioaminal
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

penicillanic acids (CHEBI:59004 )

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	0.017	ChemAxon
pKa (Strongest Acidic)	3.4	ChemAxon
pKa (Strongest Basic)	1.05	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	2	ChemAxon
Refractivity	55.84 m³·mol⁻¹	ChemAxon
Polarizability	22.82 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

7827515

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9548591

PDB ID

Not Available

ChEBI ID

59004

Good Scents ID

Not Available

References

General References

Shiho O, Nakagawa Y, Tsuchiya K: IgE antibodies for penicillins and cephalosporins in rats. II. Antigenic specificity of rat anti-penicillin-OvA IgE sera. J Antibiot (Tokyo). 1981 Jan;34(1):79-83. doi: 10.7164/antibiotics.34.79. [PubMed:6166603 ]
Baltzer B, Lund F, Rastrup-Andersen N: Degradation of mecillinam in aqueous solution. J Pharm Sci. 1979 Oct;68(10):1207-15. doi: 10.1002/jps.2600681005. [PubMed:41925 ]
LOTUS database [Link]

Showing NP-Card for (2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid (NP0264691)

MOL for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D MOL for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D SDF for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D-SDF for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

PDB for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D PDB for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

SMILES for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

INCHI for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

Structure for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D Structure for NP0264691 ((2s,5r,6r)-6-[(hydroxymethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)