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Showing NP-Card for proclavaminic acid (NP0154530)

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Record Information
Version2.0
Created at2022-09-02 11:27:37 UTC
Updated at2022-09-02 11:27:38 UTC
NP-MRD IDNP0154530
Secondary Accession NumbersNone
Natural Product Identification
Common Nameproclavaminic acid
DescriptionProclavaminic acid belongs to the class of organic compounds known as monobactams. Monobactams are compounds comprising beta-lactam ring is alone and not fused to another ring. proclavaminic acid is found in Streptomyces clavuligerus. Proclavaminic acid is a very strong basic compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0154530 (proclavaminic acid)


  Mrv0541 05041409242D          

 16 16  0  0  1  0            999 V2000
    4.4105    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6439    4.0040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5855    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8470    3.7905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8230    2.2791    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.8574    3.2071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6480    2.2791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0605    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1730    0.8502    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0605    2.9936    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4105    2.9936    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5719    2.7946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8855    1.5647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6480    0.8502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4550    1.7488    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5047    1.4667    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 10  6  1  0  0  0  0
  7 10  1  1  0  0  0
  5 11  1  6  0  0  0
 12  6  2  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
  5 15  1  6  0  0  0
  7 16  1  1  0  0  0
M  END
Download

3D MOL for NP0154530 (proclavaminic acid)

     RDKit          3D

 28 28  0  0  0  0  0  0  0  0999 V2000
    4.2745    0.3024    0.3790 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9637    0.8996    0.3313 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9278   -0.2075    0.1608 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5311    0.3722    0.1051 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5237    1.2528   -0.9967 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4489   -0.7589   -0.1322 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4803   -1.6324    1.0497 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4741   -2.3949    1.3233 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5584   -1.6713    1.9333 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7533   -0.1163   -0.3132 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5749    0.6912    0.5345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6835    0.4484   -0.4681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6551   -0.0723   -1.3946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6836   -0.3318   -2.6258 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2810   -0.6526    0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7816    0.3645   -0.5499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8174    1.4379    1.2898 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9302    1.6054   -0.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1870   -0.7990   -0.7362 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0922   -0.8658    1.0472 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3519    0.9599    0.9978 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0838    0.8287   -1.6931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1217   -1.3097   -1.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4940   -1.4037    2.9013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8534    0.2798    1.5150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3184    1.7676    0.5883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4135   -0.3305   -0.1683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1811    1.3363   -0.8585 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  4  6  1  0
  6 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
  6  7  1  0
  7  9  1  0
  7  8  2  0
 13 10  1  0
  4 21  1  1
  5 22  1  0
  3 19  1  0
  3 20  1  0
  2 17  1  0
  2 18  1  0
  1 15  1  0
  1 16  1  0
  6 23  1  6
 11 25  1  0
 11 26  1  0
 12 27  1  0
 12 28  1  0
  9 24  1  0
M  END
Download

3D SDF for NP0154530 (proclavaminic acid)


  Mrv0541 05041409242D          

 16 16  0  0  1  0            999 V2000
    4.4105    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6439    4.0040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5855    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8470    3.7905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8230    2.2791    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.8574    3.2071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6480    2.2791    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0605    1.5647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1730    0.8502    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0605    2.9936    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4105    2.9936    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5719    2.7946    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8855    1.5647    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6480    0.8502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4550    1.7488    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5047    1.4667    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  7  1  0  0  0  0
  9  3  1  0  0  0  0
 10  4  1  0  0  0  0
 10  6  1  0  0  0  0
  7 10  1  1  0  0  0
  5 11  1  6  0  0  0
 12  6  2  0  0  0  0
 13  8  2  0  0  0  0
 14  8  1  0  0  0  0
  5 15  1  6  0  0  0
  7 16  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0154530

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@](O)(CCN)[C@]([H])(N1CCC1=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H14N2O4/c9-3-1-5(11)7(8(13)14)10-4-2-6(10)12/h5,7,11H,1-4,9H2,(H,13,14)/t5-,7+/m1/s1

> <INCHI_KEY>
NMCINKPVAOXDJH-VDTYLAMSSA-N

> <FORMULA>
C8H14N2O4

> <MOLECULAR_WEIGHT>
202.2078

> <EXACT_MASS>
202.095356946

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
19.502070809937436

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R)-5-amino-3-hydroxy-2-(2-oxoazetidin-1-yl)pentanoic acid

> <ALOGPS_LOGP>
-2.86

> <JCHEM_LOGP>
-4.585853286209563

> <ALOGPS_LOGS>
0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.55772653179979

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4884448868999494

> <JCHEM_PKA_STRONGEST_BASIC>
9.5278948070983

> <JCHEM_POLAR_SURFACE_AREA>
103.86

> <JCHEM_REFRACTIVITY>
47.0072

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.21e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
proclavaminic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0154530 (proclavaminic acid)

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PDB for NP0154530 (proclavaminic acid)
HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   10  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    6                                                       
CONECT    3    1    9                                                       
CONECT    4    2   10                                                       
CONECT    5    1    7   11   15                                             
CONECT    6    2   10   12                                                  
CONECT    7    5    8   10   16                                             
CONECT    8    7   13   14                                                  
CONECT    9    3                                                            
CONECT   10    4    6    7                                                  
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15    5                                                            
CONECT   16    7                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

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3D PDB for NP0154530 (proclavaminic acid)
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SMILES for NP0154530 (proclavaminic acid)
[H][C@@](O)(CCN)[C@]([H])(N1CCC1=O)C(O)=O
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INCHI for NP0154530 (proclavaminic acid)
InChI=1S/C8H14N2O4/c9-3-1-5(11)7(8(13)14)10-4-2-6(10)12/h5,7,11H,1-4,9H2,(H,13,14)/t5-,7+/m1/s1
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View in JSmol
Synonyms
ValueSource
5-Amino-2,4,5-trideoxy-2-(2-oxo-1-azetidinyl)-D-threo-pentonic acidChEBI
5-AMINO-3-hydroxy-2-(2-oxo-azetidin-1-yl)-pentanoIC ACIDChEBI
ProclavaminateChEBI
5-Amino-2,4,5-trideoxy-2-(2-oxo-1-azetidinyl)-D-threo-pentonateGenerator
5-AMINO-3-hydroxy-2-(2-oxo-azetidin-1-yl)-pentanoateGenerator
Chemical FormulaC8H14N2O4
Average Mass202.2078 Da
Monoisotopic Mass202.09536 Da
IUPAC Name(2S,3R)-5-amino-3-hydroxy-2-(2-oxoazetidin-1-yl)pentanoic acid
Traditional Nameproclavaminic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](O)(CCN)[C@]([H])(N1CCC1=O)C(O)=O
InChI Identifier
InChI=1S/C8H14N2O4/c9-3-1-5(11)7(8(13)14)10-4-2-6(10)12/h5,7,11H,1-4,9H2,(H,13,14)/t5-,7+/m1/s1
InChI KeyNMCINKPVAOXDJH-VDTYLAMSSA-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 monobactams. Monobactams are compounds comprising beta-lactam ring is alone and not fused to another ring.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactams  
Sub ClassBeta lactams  
Direct ParentMonobactams  
Alternative Parents
Substituents
  • Monobactam
    • 

  • Alpha-amino acid or derivatives
    • 

  • Beta-hydroxy acid
    • 

  • Heterocyclic fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Fatty acid
    • 

  • Fatty acyl
    • 

  • Tertiary carboxylic acid amide
    • 

  • 1,3-aminoalcohol
    • 

  • Secondary alcohol
    • 

  • Amino acid or derivatives
    • 

  • Azetidine
    • 

  • Carboxamide group
    • 

  • Amino acid
    • 

  • Azacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Hydrocarbon derivative
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Primary aliphatic amine
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Primary amine
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-2.9ALOGPS
logP-4.6ChemAxon
logS0.04ALOGPS
pKa (Strongest Acidic)3.49ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area103.86 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity47.01 m³·mol⁻¹ChemAxon
Polarizability19.5 ųChemAxon
Number of Rings1ChemAxon
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 IDNot Available
KEGG Compound IDC06658  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound194953  
PDB IDNot Available
ChEBI ID15425  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]