NP-MRD: Showing NP-Card for pinocicolin A (NP0350824)

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Record Information

Version

2.0

Created at

2025-03-12 00:45:24 UTC

Updated at

2025-06-10 23:53:18 UTC

NP-MRD ID

NP0350824

Natural Product DOI

https://doi.org/10.57994/3809

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pinocicolin A

Description

Based on a literature review very few articles have been published on pinocicolin A.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 06092300522D          

 28 27  0  0  1  0            999 V2000
    6.3704    7.4147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2421    8.2296    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4722    8.5260    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3438    9.3409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8305    8.0074    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0606    8.3037    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9323    9.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4190    7.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6491    8.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0074    7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    7.8592    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5959    7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1741    7.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7242    6.5256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1092    8.6741    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.9809    9.4891    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    2.1358    6.7479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9589    7.1924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8837    8.7482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6536    8.4519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2953    8.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0652    8.6741    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.7068    9.1927    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   10.3484    9.7114    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    9.1935    7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9634    7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5519    7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1669    9.7854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 11 15  1  6  0  0  0
 15 16  3  0  0  0  0
 10 17  2  0  0  0  0
  5 18  1  6  0  0  0
  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  3  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 21 28  2  0  0  0  0
M  CHG  4  15   1  16  -1  23   1  24  -1
M  END


  Mrv2104 06092300522D          

 28 27  0  0  1  0            999 V2000
    6.3704    7.4147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2421    8.2296    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.4722    8.5260    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.3438    9.3409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8305    8.0074    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0606    8.3037    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9323    9.1187    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4190    7.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6491    8.0814    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0074    7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    7.8592    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5959    7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1741    7.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7242    6.5256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1092    8.6741    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.9809    9.4891    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    2.1358    6.7479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9589    7.1924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8837    8.7482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6536    8.4519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2953    8.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0652    8.6741    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.7068    9.1927    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   10.3484    9.7114    0.0000 C   0  5  0  0  0  0  0  0  0  0  0  0
    9.1935    7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9634    7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5519    7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1669    9.7854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  3  4  1  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 11 15  1  6  0  0  0
 15 16  3  0  0  0  0
 10 17  2  0  0  0  0
  5 18  1  6  0  0  0
  2 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  3  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 21 28  2  0  0  0  0
M  CHG  4  15   1  16  -1  23   1  24  -1
M  END
> <DATABASE_ID>
NP0350824

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@H]([N+]#[C-])C(=O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COC(=O)[C@@H]([N+]#[C-])C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C18H28N2O8/c1-9(2)13(19-5)17(25)27-7-11(21)15(23)16(24)12(22)8-28-18(26)14(20-6)10(3)4/h9-16,21-24H,7-8H2,1-4H3/t11-,12-,13+,14+,15-,16-/m1/s1

> <INCHI_KEY>
HAKYKRGPXWDGKY-OWDFPOFWSA-N

> <FORMULA>
C18H28N2O8

> <MOLECULAR_WEIGHT>
400.428

> <EXACT_MASS>
400.18456587

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
40.21654769900819

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2,3,4,5-tetrahydroxy-6-{[(2S)-2-isocyano-3-methylbutanoyl]oxy}hexyl (2S)-2-isocyano-3-methylbutanoate

> <JCHEM_LOGP>
-4.44940906175189

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
13.384288457344994

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.57994494260027

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5328797607680227

> <JCHEM_POLAR_SURFACE_AREA>
142.24

> <JCHEM_REFRACTIVITY>
113.5906

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R,5R)-2,3,4,5-tetrahydroxy-6-{[(2S)-2-isocyano-3-methylbutanoyl]oxy}hexyl (2S)-2-isocyano-3-methylbutanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JUN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUN-23         0                                  
HETATM    1  O   UNK     0      11.891  13.841   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      11.652  15.362   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.215  15.915   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       9.975  17.436   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.017  14.947   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.580  15.500   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.340  17.022   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.382  14.532   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       4.945  15.085   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.747  14.117   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.310  14.670   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.112  13.702   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.325  14.256   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.352  12.181   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       2.070  16.192   0.000  0.00  0.00           N+1
HETATM   16  C   UNK     0       1.831  17.713   0.000  0.00  0.00           C-1
HETATM   17  O   UNK     0       3.987  12.596   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       9.257  13.426   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      12.850  16.330   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      14.287  15.777   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      15.484  16.745   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      16.922  16.192   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      18.119  17.160   0.000  0.00  0.00           N+1
HETATM   24  C   UNK     0      19.317  18.128   0.000  0.00  0.00           C-1
HETATM   25  C   UNK     0      17.161  14.670   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      18.598  14.117   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      15.964  13.702   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      15.245  18.266   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   18                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12   15                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15   11   16                                                       
CONECT   16   15                                                            
CONECT   17   10                                                            
CONECT   18    5                                                            
CONECT   19    2   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   28                                                  
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   21                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₂₈N₂O₈

Average Mass

400.4280 Da

Monoisotopic Mass

400.18457 Da

IUPAC Name

(2R,3R,4R,5R)-2,3,4,5-tetrahydroxy-6-{[(2S)-2-isocyano-3-methylbutanoyl]oxy}hexyl (2S)-2-isocyano-3-methylbutanoate

Traditional Name

(2R,3R,4R,5R)-2,3,4,5-tetrahydroxy-6-{[(2S)-2-isocyano-3-methylbutanoyl]oxy}hexyl (2S)-2-isocyano-3-methylbutanoate

CAS Registry Number

Not Available

SMILES

CC(C)[C@H]([N+]#[C-])C(=O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COC(=O)[C@@H]([N+]#[C-])C(C)C

InChI Identifier

InChI=1S/C18H28N2O8/c1-9(2)13(19-5)17(25)27-7-11(21)15(23)16(24)12(22)8-28-18(26)14(20-6)10(3)4/h9-16,21-24H,7-8H2,1-4H3/t11-,12-,13+,14+,15-,16-/m1/s1

InChI Key

HAKYKRGPXWDGKY-OWDFPOFWSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	kishimoto@u-shizuoka-ken.ac.jp	University of Shizuoka	Shinji Kishimoto	2025-03-12	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	kishimoto@u-shizuoka-ken.ac.jp	University of Shizuoka	Shinji Kishimoto	2025-03-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, CD3OD, experimental)	kishimoto@u-shizuoka-ken.ac.jp	University of Shizuoka	Shinji Kishimoto	2025-03-12	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	kishimoto@u-shizuoka-ken.ac.jp	University of Shizuoka	Shinji Kishimoto	2025-03-12	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	kishimoto@u-shizuoka-ken.ac.jp	University of Shizuoka	Shinji Kishimoto	2025-03-12	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Penicillium pinophilum		Not Available

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	-4.4	ChemAxon
pKa (Strongest Acidic)	12.58	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	142.24 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	113.59 m³·mol⁻¹	ChemAxon
Polarizability	40.22 Å³	ChemAxon
Number of Rings	0	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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for pinocicolin A (NP0350824)

MOL for NP0350824 (pinocicolin A)

3D MOL for NP0350824 (pinocicolin A)

3D SDF for NP0350824 (pinocicolin A)

3D-SDF for NP0350824 (pinocicolin A)

PDB for NP0350824 (pinocicolin A)

3D PDB for NP0350824 (pinocicolin A)

SMILES for NP0350824 (pinocicolin A)

INCHI for NP0350824 (pinocicolin A)

Structure for NP0350824 (pinocicolin A)

3D Structure for NP0350824 (pinocicolin A)