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Showing NP-Card for clavaldehyde (NP0265751)

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Record Information
Version2.0
Created at2022-09-08 09:50:49 UTC
Updated at2022-09-08 09:50:49 UTC
NP-MRD IDNP0265751
Secondary Accession NumbersNone
Natural Product Identification
Common Nameclavaldehyde
DescriptionClavaldehyde 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. Clavaldehyde is an extremely weak basic (essentially neutral) compound (based on its pKa). clavaldehyde is found in Streptomyces clavuligerus. clavaldehyde was first documented in 2002 (PMID: 12426344). An organic heterobicyclic compound that is clavulanic acid in which the allylic alcohol group has been oxidised to the corresponding aldehyde (PMID: 29062960) (PMID: 19941870) (PMID: 16251194) (PMID: 17279617).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0265751 (clavaldehyde)


  Mrv1652305232000042D          

 14 15  0  0  1  0            999 V2000
   -0.9664    0.2614    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    0.0139    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9664    1.0865    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7914    0.2614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123    0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826   -0.8110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    1.3340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7914    1.0865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1373    0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7601   -1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3948   -1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3748   -0.3218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5499    1.3885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748    1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  1  0  0  0
  3  8  1  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  6 11  2  0  0  0  0
  4  8  1  0  0  0  0
  5  7  1  0  0  0  0
  4 12  2  0  0  0  0
  9 13  1  0  0  0  0
 13 14  2  0  0  0  0
M  END
Download

3D MOL for NP0265751 (clavaldehyde)

     RDKit          3D

 21 22  0  0  0  0  0  0  0  0999 V2000
    2.5583   -2.3885   -0.0854 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0488   -1.2510   -0.0978 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2106   -0.0760   -0.1821 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020   -0.2259   -0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1351   -1.3835   -0.2484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1086   -1.0528    0.2594 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3089   -1.4395   -0.5784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7374   -0.0724   -0.2436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7918    0.5355   -0.0424 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3738    0.2917   -0.2438 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0433    0.9031   -0.3352 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0806    1.8460    0.8033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8205    2.0440    1.6576 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2610    2.5607    0.9456 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177   -1.1314   -0.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6521    0.9155   -0.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2875   -1.1795    1.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9110   -2.2664   -0.1723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0645   -1.5063   -1.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0592    1.4390   -1.3201 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4218    3.4378    0.4433 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 12  1  0
 12 13  2  0
 12 11  1  0
 11 10  1  0
 10  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  4 11  1  0
  8 10  1  0
 14 21  1  0
 11 20  1  6
  6 17  1  1
  7 18  1  0
  7 19  1  0
  3 16  1  0
  2 15  1  0
M  END
Download

3D SDF for NP0265751 (clavaldehyde)


  Mrv1652305232000042D          

 14 15  0  0  1  0            999 V2000
   -0.9664    0.2614    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    0.0139    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9664    1.0865    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7914    0.2614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3123    0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826   -0.8110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1826    1.3340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7914    1.0865    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1373    0.6740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7601   -1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3948   -1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3748   -0.3218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5499    1.3885    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748    1.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  1  0  0  0
  3  8  1  0  0  0  0
  5  9  2  0  0  0  0
  6 10  1  0  0  0  0
  6 11  2  0  0  0  0
  4  8  1  0  0  0  0
  5  7  1  0  0  0  0
  4 12  2  0  0  0  0
  9 13  1  0  0  0  0
 13 14  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0265751

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@@H]1N2[C@@H](CC2=O)O\C1=C/C=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1-2,6-7H,3H2,(H,12,13)/b4-1-/t6-,7-/m1/s1

> <INCHI_KEY>
NABDJFSYSZIMMH-PBFISZAISA-N

> <FORMULA>
C8H7NO5

> <MOLECULAR_WEIGHT>
197.146

> <EXACT_MASS>
197.032422329

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
17.382548400679937

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.26

> <JCHEM_LOGP>
-1.3595492773333333

> <ALOGPS_LOGS>
-0.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.23303675519318

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1753811584688716

> <JCHEM_PKA_STRONGEST_BASIC>
-4.673345399792547

> <JCHEM_POLAR_SURFACE_AREA>
83.91

> <JCHEM_REFRACTIVITY>
43.194500000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.45e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3Z,5R)-7-oxo-3-(2-oxoethylidene)-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0265751 (clavaldehyde)

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PDB for NP0265751 (clavaldehyde)
HEADER    PROTEIN                                 23-MAY-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-20         0                                  
HETATM    1  N   UNK     0      -1.804   0.488   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -0.341   0.026   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.804   2.028   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.344   0.488   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.583   1.258   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.341  -1.514   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.341   2.490   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.344   2.028   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.123   1.258   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.419  -2.592   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.737  -2.592   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -4.433  -0.601   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.893   2.592   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.433   2.592   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    8   12                                                  
CONECT    5    2    9    7                                                  
CONECT    6    2   10   11                                                  
CONECT    7    3    5                                                       
CONECT    8    3    4                                                       
CONECT    9    5   13                                                       
CONECT   10    6                                                            
CONECT   11    6                                                            
CONECT   12    4                                                            
CONECT   13    9   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

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3D PDB for NP0265751 (clavaldehyde)
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SMILES for NP0265751 (clavaldehyde)
OC(=O)[C@@H]1N2[C@@H](CC2=O)O\C1=C/C=O
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INCHI for NP0265751 (clavaldehyde)
InChI=1S/C8H7NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1-2,6-7H,3H2,(H,12,13)/b4-1-/t6-,7-/m1/s1
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View in JSmol
Synonyms
ValueSource
(3R,5R)-Clavulanate-9-aldehydeChEBI
(3R,5R)-Clavulanic acid-9-aldehydeChEBI
Clavulanate-9-aldehydeChEBI
Clavulanic acid-9-aldehydeGenerator
Chemical FormulaC8H7NO5
Average Mass197.1460 Da
Monoisotopic Mass197.03242 Da
IUPAC Name(2R,3Z,5R)-7-oxo-3-(2-oxoethylidene)-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Traditional Name(2R,3Z,5R)-7-oxo-3-(2-oxoethylidene)-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)[C@@H]1N2[C@@H](CC2=O)O\C1=C/C=O
InChI Identifier
InChI=1S/C8H7NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1-2,6-7H,3H2,(H,12,13)/b4-1-/t6-,7-/m1/s1
InChI KeyNABDJFSYSZIMMH-PBFISZAISA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces clavuligerusLOTUS Database
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.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
    • 

  • Clavam
    • 

  • Para-oxazepine
    • 

  • Alpha,beta-unsaturated aldehyde
    • 

  • Beta-lactam
    • 

  • Enal
    • 

  • Vinylogous ester
    • 

  • Tertiary carboxylic acid amide
    • 

  • Oxazolidine
    • 

  • Azetidine
    • 

  • Carboxamide group
    • 

  • Lactam
    • 

  • Oxacycle
    • 

  • Carboxylic acid
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Aldehyde
    • 

  • Organic nitrogen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organonitrogen compound
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.26ALOGPS
logP-1.4ChemAxon
logS-0.13ALOGPS
pKa (Strongest Acidic)3.18ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area83.91 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity43.19 m³·mol⁻¹ChemAxon
Polarizability17.38 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID30791256  
KEGG Compound IDC06661  
BioCyc IDCPD-9260  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound15517793  
PDB IDNot Available
ChEBI ID27819  
Good Scents IDNot Available
References
General References
  1. de la Fuente A, Lorenzana LM, Martin JF, Liras P: Mutants of Streptomyces clavuligerus with disruptions in different genes for clavulanic acid biosynthesis produce large amounts of holomycin: possible cross-regulation of two unrelated secondary metabolic pathways. J Bacteriol. 2002 Dec;184(23):6559-65. doi: 10.1128/JB.184.23.6559-6565.2002. [PubMed:12426344  ] 
  2. Unsaldi E, Kurt-Kizildogan A, Voigt B, Becher D, Ozcengiz G: Proteome-wide alterations in an industrial clavulanic acid producing strain of Streptomyces clavuligerus. Synth Syst Biotechnol. 2016 Nov 6;2(1):39-48. doi: 10.1016/j.synbio.2016.10.003.  eCollection 2017 Mar. [PubMed:29062960  ] 
  3. Mackenzie AK, Valegard K, Iqbal A, Caines ME, Kershaw NJ, Jensen SE, Schofield CJ, Andersson I: Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid. J Mol Biol. 2010 Feb 19;396(2):332-44. doi: 10.1016/j.jmb.2009.11.045. Epub 2009  Nov 24. [PubMed:19941870  ] 
  4. Arulanantham H, Kershaw NJ, Hewitson KS, Hughes CE, Thirkettle JE, Schofield CJ: ORF17 from the clavulanic acid biosynthesis gene cluster catalyzes the ATP-dependent formation of N-glycyl-clavaminic acid. J Biol Chem. 2006 Jan 6;281(1):279-87. doi: 10.1074/jbc.M507711200. Epub 2005 Oct  26. [PubMed:16251194  ] 
  5. MacKenzie AK, Kershaw NJ, Hernandez H, Robinson CV, Schofield CJ, Andersson I: Clavulanic acid dehydrogenase: structural and biochemical analysis of the final step in the biosynthesis of the beta-lactamase inhibitor clavulanic acid. Biochemistry. 2007 Feb 13;46(6):1523-33. doi: 10.1021/bi061978x. Epub 2007 Jan  19. [PubMed:17279617  ] 
  6. LOTUS database [Link]