NP-MRD: Showing NP-Card for Clavulanic acid (NP0023254)

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Record Information

Version

2.0

Created at

2021-01-06 08:21:46 UTC

Updated at

2021-07-15 17:41:15 UTC

NP-MRD ID

NP0023254

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Clavulanic acid

Provided By

NPAtlas

Description

Isoclavulanic acid is also known as isoclavulanate. Clavulanic acid is found in Streptomyces and Streptomyces clavuligerus ATCC 27064. Clavulanic acid was first documented in 1977 (PMID: 879738). Based on a literature review very few articles have been published on Isoclavulanic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105403D          

 23 24  0  0  0  0            999 V2000
   -1.1407    2.2649    1.3557 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1392    1.7836    0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1072    2.3153    1.1057 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1972    0.6640   -0.1445 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4295   -0.5650    0.3243 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6943   -0.8981    0.2036 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7084   -0.0496   -0.4478 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2197   -0.8076   -1.5288 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5317   -1.3383    0.9259 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7732   -0.7550    0.7458 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7025   -1.3460   -0.2862 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8996    0.0741   -0.6296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8035    0.8081   -1.0329 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5583    0.2802   -0.2936 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4861    3.1004    0.5615 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2980    0.9595   -1.0963 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0507   -1.8572    0.5997 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3238    0.8664   -0.8841 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5831    0.1071    0.2368 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8234   -1.5090   -1.2215 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2798   -0.3576    1.6509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5806   -1.8791    0.1062 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1179   -1.8611   -1.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  5  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14  4  1  0  0  0  0
 14 10  1  0  0  0  0
  3 15  1  0  0  0  0
  4 16  1  6  0  0  0
  6 17  1  0  0  0  0
  7 18  1  0  0  0  0
  7 19  1  0  0  0  0
  8 20  1  0  0  0  0
 10 21  1  1  0  0  0
 11 22  1  0  0  0  0
 11 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0023254

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]1([H])N2C(=O)C([H])([H])[C@@]2([H])O\C1=C(/[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C8H9NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1,6-7,10H,2-3H2,(H,12,13)/b4-1+/t6-,7-/m1/s1

> <INCHI_KEY>
HZZVJAQRINQKSD-INJCQMSSSA-N

> <FORMULA>
C8H9NO5

> <MOLECULAR_WEIGHT>
199.162

> <EXACT_MASS>
199.048072394

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.072290143074603

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3E,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
-1.16

> <JCHEM_LOGP>
-1.521207563

> <ALOGPS_LOGS>
0.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.522017294386345

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3169081461310097

> <JCHEM_PKA_STRONGEST_BASIC>
-2.572438391835412

> <JCHEM_POLAR_SURFACE_AREA>
87.07000000000001

> <JCHEM_REFRACTIVITY>
44.252500000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.37e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isoclavulanic acid

> <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  O   UNK     0      -1.141   2.265   1.356  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.139   1.784   0.811  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.107   2.315   1.106  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.197   0.664  -0.145  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.430  -0.565   0.324  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.694  -0.898   0.204  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.708  -0.050  -0.448  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.220  -0.808  -1.529  0.00  0.00           O+0
HETATM    9  O   UNK     0      -0.532  -1.338   0.926  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.773  -0.755   0.746  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.703  -1.346  -0.286  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.900   0.074  -0.630  0.00  0.00           C+0
HETATM   13  O   UNK     0      -3.804   0.808  -1.033  0.00  0.00           O+0
HETATM   14  N   UNK     0      -1.558   0.280  -0.294  0.00  0.00           N+0
HETATM   15  H   UNK     0       1.486   3.100   0.562  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.298   0.960  -1.096  0.00  0.00           H+0
HETATM   17  H   UNK     0       2.051  -1.857   0.600  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.324   0.866  -0.884  0.00  0.00           H+0
HETATM   19  H   UNK     0       3.583   0.107   0.237  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.823  -1.509  -1.222  0.00  0.00           H+0
HETATM   21  H   UNK     0      -2.280  -0.358   1.651  0.00  0.00           H+0
HETATM   22  H   UNK     0      -3.581  -1.879   0.106  0.00  0.00           H+0
HETATM   23  H   UNK     0      -2.118  -1.861  -1.062  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   15                                                       
CONECT    4    2    5   14   16                                             
CONECT    5    4    6    9                                                  
CONECT    6    5    7   17                                                  
CONECT    7    6    8   18   19                                             
CONECT    8    7   20                                                       
CONECT    9    5   10                                                       
CONECT   10    9   11   14   21                                             
CONECT   11   10   12   22   23                                             
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12    4   10                                                  
CONECT   15    3                                                            
CONECT   16    4                                                            
CONECT   17    6                                                            
CONECT   18    7                                                            
CONECT   19    7                                                            
CONECT   20    8                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   11                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Isoclavulanate	Generator
(2R,3E,5R)-3-(2-Hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator

Chemical Formula

C₈H₉NO₅

Average Mass

199.1620 Da

Monoisotopic Mass

199.04807 Da

IUPAC Name

(2R,3E,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

isoclavulanic acid

CAS Registry Number

Not Available

SMILES

OC\C=C1\O[C@@H]2CC(=O)N2[C@H]1C(O)=O

InChI Identifier

InChI=1S/C8H9NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1,6-7,10H,2-3H2,(H,12,13)/b4-1+/t6-,7-/m1/s1

InChI Key

HZZVJAQRINQKSD-INJCQMSSSA-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	NPAtlas	879738
Streptomyces clavuligerus	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	ALOGPS
logP	-1.5	ChemAxon
logS	0.23	ALOGPS
pKa (Strongest Acidic)	3.32	ChemAxon
pKa (Strongest Basic)	-2.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	87.07 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	44.25 m³·mol⁻¹	ChemAxon
Polarizability	18.07 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

NPA019639

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4444478

KEGG Compound ID

C11833

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281002

PDB ID

Not Available

ChEBI ID

29607

Good Scents ID

Not Available

References

General References

Reading C, Cole M: Clavulanic acid: a beta-lactamase-inhiting beta-lactam from Streptomyces clavuligerus. Antimicrob Agents Chemother. 1977 May;11(5):852-7. doi: 10.1128/aac.11.5.852. [PubMed:879738 ]

Showing NP-Card for Clavulanic acid (NP0023254)

MOL for NP0023254 (Clavulanic acid)

3D MOL for NP0023254 (Clavulanic acid)

3D SDF for NP0023254 (Clavulanic acid)

3D-SDF for NP0023254 (Clavulanic acid)

PDB for NP0023254 (Clavulanic acid)

3D PDB for NP0023254 (Clavulanic acid)

SMILES for NP0023254 (Clavulanic acid)

INCHI for NP0023254 (Clavulanic acid)

Structure for NP0023254 (Clavulanic acid)

3D Structure for NP0023254 (Clavulanic acid)