NP-MRD: Showing NP-Card for (2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid (NP0286331)

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Record Information

Version

2.0

Created at

2022-09-09 14:51:33 UTC

Updated at

2022-09-09 14:51:33 UTC

NP-MRD ID

NP0286331

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Description

(2S,3Z,5S)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]Heptane-2-carboxylic acid 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,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid is found in Streptomyces clavuligerus. Based on a literature review very few articles have been published on (2S,3Z,5S)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]Heptane-2-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 28 29  0  0  0  0  0  0  0  0999 V2000
    4.9849   -0.6329    0.6830 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7053   -1.2711    0.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6145   -0.2793    0.3357 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6859    0.7408   -0.5939 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6013   -0.3374    1.1270 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5644    0.6177    1.0640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5965    0.2415    0.5799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0372   -0.9837    0.0864 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2282   -0.7586   -0.6540 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.3730   -1.6983   -0.3625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0713   -0.4619    0.1301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2615   -0.1658    0.3773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8543    0.2588    0.2123 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7678    1.1813    0.4689 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5454    2.0430   -0.6975 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6349    2.9086   -0.6501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2997    1.9382   -1.8461 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7138   -1.3540    0.4858 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1224    0.1260   -0.0270 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8373   -1.7519   -0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5196   -2.0455    1.1652 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5466    1.2660   -0.6747 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7652    1.6298    1.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1169   -0.4014   -1.6727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8478   -2.0107   -1.3085 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2016   -2.4606    0.3968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9178    1.7498    1.4046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9073    1.9116   -2.7755 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 17  1  0
 15 16  2  0
 14  7  1  0
 13  9  1  0
  1 18  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  4 22  1  0
  6 23  1  0
  9 24  1  6
 10 25  1  0
 10 26  1  0
 14 27  1  1
 17 28  1  0
M  END


  Mrv1652309092216512D          

 17 18  0  0  1  0            999 V2000
    5.2469   -0.0842    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4219   -0.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0094    0.6303    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4219    1.3448    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1844    0.6303    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7719    1.3448    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
    1.4620    0.6773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6773    0.9323    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1477    0.9323    0.0000 C   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  2  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
    2.5239    2.9684    0.0000 O   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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  2  0  0  0  0
  5  6  1  4  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
  9 13  1  1  0  0  0
 13 14  1  0  0  0  0
  7 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0286331

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCC(O)=N\C=C1/O[C@H]2CC(=O)N2[C@@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H11N3O5/c10-2-5(13)11-3-4-8(9(15)16)12-6(14)1-7(12)17-4/h3,7-8H,1-2,10H2,(H,11,13)(H,15,16)/b4-3-/t7-,8-/m0/s1

> <INCHI_KEY>
ZKEFDYULAFPJFJ-FBJRUSGASA-N

> <FORMULA>
C9H11N3O5

> <MOLECULAR_WEIGHT>
241.203

> <EXACT_MASS>
241.069870466

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
22.502326208447336

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3Z,5S)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_LOGP>
-4.7344064641042385

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.8029114416882734

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1272541687739532

> <JCHEM_PKA_STRONGEST_BASIC>
9.041134965024648

> <JCHEM_POLAR_SURFACE_AREA>
125.45

> <JCHEM_REFRACTIVITY>
53.764700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3Z,5S)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  N   UNK     0       9.794  -0.157   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.254  -0.157   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.484   1.177   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.254   2.510   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       5.944   1.177   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       5.174   2.510   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.634   2.510   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.729   1.264   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.264   1.740   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.276   1.740   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.276   3.280   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.365   4.369   0.000  0.00  0.00           O+0
HETATM   13  N   UNK     0       1.264   3.280   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.729   3.756   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.205   5.221   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.711   5.541   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.174   6.365   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11    9   14                                                  
CONECT   14   13    7   15                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Value	Source
(2S,3Z,5S)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator

Chemical Formula

C₉H₁₁N₃O₅

Average Mass

241.2030 Da

Monoisotopic Mass

241.06987 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

NCC(O)=N\C=C1/O[C@H]2CC(=O)N2[C@@H]1C(O)=O

InChI Identifier

InChI=1S/C9H11N3O5/c10-2-5(13)11-3-4-8(9(15)16)12-6(14)1-7(12)17-4/h3,7-8H,1-2,10H2,(H,11,13)(H,15,16)/b4-3-/t7-,8-/m0/s1

InChI Key

ZKEFDYULAFPJFJ-FBJRUSGASA-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
Streptomyces clavuligerus	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
Clavam
Para-oxazepine
Tertiary carboxylic acid amide
Oxazolidine
Beta-lactam
Amino acid
Lactam
Carboxamide group
Azetidine
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Monocarboxylic acid or derivatives
Carboxylic acid
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
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

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163190015

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid (NP0286331)

MOL for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D MOL for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D SDF for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D-SDF for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

PDB for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D PDB for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

SMILES for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

INCHI for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

Structure for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)

3D Structure for NP0286331 ((2s,3z,5s)-3-{[(2-amino-1-hydroxyethylidene)amino]methylidene}-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid)