NP-MRD: Showing NP-Card for syn-Copalyl diphosphate (NP0338638)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2024-09-11 16:35:18 UTC

Updated at

2024-09-11 16:35:19 UTC

NP-MRD ID

NP0338638

Secondary Accession Numbers

None

Natural Product Identification

Common Name

syn-Copalyl diphosphate

Description

Syn-Copalyl diphosphate belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Syn-Copalyl diphosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241221492D          

 30 31  0  0  1  0            999 V2000
    1.6248  -11.7938    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6213  -12.6188    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3464  -11.3864    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9065  -11.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6180  -10.9791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9065  -13.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3396  -13.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503  -11.8006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3498  -10.5575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1918  -11.7938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1918  -12.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1174  -13.8307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6855  -13.8307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503  -12.6256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4543  -11.5381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0646  -10.1467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7794  -10.5716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7684  -11.3898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4900  -10.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4764  -11.8041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1947  -11.4034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0163  -11.4000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.8413  -11.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0129  -10.5751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0129  -12.2250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6703  -11.4000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4952  -11.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6669  -10.5751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6669  -12.2250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6180  -13.4404    0.0000 H   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
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3  9  1  6  0  0  0
  4 10  1  0  0  0  0
  6 11  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  1  0  0  0  0
  7 14  1  0  0  0  0
  8 15  2  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 22 25  2  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  2  0  0  0  0
  8 14  1  0  0  0  0
 10 11  1  0  0  0  0
  2 30  1  6  0  0  0
M  END


  Mrv0541 02241221492D          

 30 31  0  0  1  0            999 V2000
    1.6248  -11.7938    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6213  -12.6188    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3464  -11.3864    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9065  -11.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6180  -10.9791    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9065  -13.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3396  -13.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503  -11.8006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3498  -10.5575    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1918  -11.7938    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1918  -12.6188    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1174  -13.8307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6855  -13.8307    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0503  -12.6256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4543  -11.5381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0646  -10.1467    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7794  -10.5716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7684  -11.3898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4900  -10.1643    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4764  -11.8041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1947  -11.4034    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0163  -11.4000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    6.8413  -11.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0129  -10.5751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0129  -12.2250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6703  -11.4000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.4952  -11.4000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6669  -10.5751    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6669  -12.2250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6180  -13.4404    0.0000 H   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
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3  9  1  6  0  0  0
  4 10  1  0  0  0  0
  6 11  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  1  0  0  0  0
  7 14  1  0  0  0  0
  8 15  2  0  0  0  0
  9 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 22 25  2  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  2  0  0  0  0
  8 14  1  0  0  0  0
 10 11  1  0  0  0  0
  2 30  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0338638

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CC[C@@H]1C(=C)CC[C@@]2([H])C(C)(C)CCC[C@]12C)=C/COP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H36O7P2/c1-15(11-14-26-29(24,25)27-28(21,22)23)7-9-17-16(2)8-10-18-19(3,4)12-6-13-20(17,18)5/h11,17-18H,2,6-10,12-14H2,1,3-5H3,(H,24,25)(H2,21,22,23)/b15-11+/t17-,18+,20-/m1/s1

> <INCHI_KEY>
JCAIWDXKLCEQEO-HZEYQZKKSA-N

> <FORMULA>
C20H36O7P2

> <MOLECULAR_WEIGHT>
450.4432

> <EXACT_MASS>
450.19362653

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
45.381870617258116

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[({[(2E)-5-[(1R,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
3.50

> <JCHEM_LOGP>
4.613945935999999

> <ALOGPS_LOGS>
-4.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.184340614405425

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186921378312

> <JCHEM_POLAR_SURFACE_AREA>
113.28999999999999

> <JCHEM_REFRACTIVITY>
113.79959999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.22e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
syn-copalyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       3.033 -22.015   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.026 -23.555   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.380 -21.255   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.692 -21.248   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.020 -20.494   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.692 -24.328   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.367 -24.335   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.694 -22.028   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.386 -19.707   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.358 -22.015   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.358 -23.555   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.086 -25.817   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.280 -25.817   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.694 -23.568   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.448 -21.538   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.721 -18.941   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.055 -19.734   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.034 -21.261   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.381 -18.973   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.356 -22.034   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.697 -21.286   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0      11.230 -21.280   0.000  0.00  0.00           P+0
HETATM   23  O   UNK     0      12.770 -21.280   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      11.224 -19.740   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      11.224 -22.820   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0      14.318 -21.280   0.000  0.00  0.00           P+0
HETATM   27  O   UNK     0      15.858 -21.280   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      14.312 -19.740   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      14.312 -22.820   0.000  0.00  0.00           O+0
HETATM   30  H   UNK     0       3.020 -25.089   0.000  0.00  0.00           H+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7   30                                             
CONECT    3    1    8    9                                                  
CONECT    4    1   10                                                       
CONECT    5    1                                                            
CONECT    6    2   11   12   13                                             
CONECT    7    2   14                                                       
CONECT    8    3   15   14                                                  
CONECT    9    3   16                                                       
CONECT   10    4   11                                                       
CONECT   11    6   10                                                       
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    7    8                                                       
CONECT   15    8                                                            
CONECT   16    9   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   20                                                       
CONECT   19   17                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24   25                                             
CONECT   23   22   26                                                       
CONECT   24   22                                                            
CONECT   25   22                                                            
CONECT   26   23   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26                                                            
CONECT   30    2                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   62    0
END

View in JSmol

Synonyms

Value	Source
Syn-copalyl diphosphoric acid	Generator
Syn-copalyl diphosphate	ChEBI
9a-Copalyl diphosphate	Generator
9a-Copalyl diphosphoric acid	Generator
9alpha-Copalyl diphosphoric acid	Generator
9α-copalyl diphosphate	Generator
9α-copalyl diphosphoric acid	Generator

Chemical Formula

C₂₀H₃₆O₇P₂

Average Mass

450.4432 Da

Monoisotopic Mass

450.19363 Da

IUPAC Name

[({[(2E)-5-[(1R,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

syn-copalyl diphosphate

CAS Registry Number

Not Available

SMILES

C\C(CC[C@@H]1C(=C)CC[C@@]2([H])C(C)(C)CCC[C@]12C)=C/COP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C20H36O7P2/c1-15(11-14-26-29(24,25)27-28(21,22)23)7-9-17-16(2)8-10-18-19(3,4)12-6-13-20(17,18)5/h11,17-18H,2,6-10,12-14H2,1,3-5H3,(H,24,25)(H2,21,22,23)/b15-11+/t17-,18+,20-/m1/s1

InChI Key

JCAIWDXKLCEQEO-HZEYQZKKSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Labdane diterpenoid
Organic pyrophosphate
Isoprenoid phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

copalyl diphosphate (CHEBI:29739 )
Labdane and halimane diterpenoids (C11902 )
Labdanes (C11902 )
Labdane and halimane diterpenoids (LMPR0104030003 )

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	3.5	ALOGPS
logP	4.61	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	113.8 m³·mol⁻¹	ChemAxon
Polarizability	45.38 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

FDB001470

KNApSAcK ID

C00000899

Chemspider ID

Not Available

KEGG Compound ID

C11902

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281991

PDB ID

Not Available

ChEBI ID

29739

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for syn-Copalyl diphosphate (NP0338638)

MOL for NP0338638 (syn-Copalyl diphosphate)

3D MOL for NP0338638 (syn-Copalyl diphosphate)

3D SDF for NP0338638 (syn-Copalyl diphosphate)

3D-SDF for NP0338638 (syn-Copalyl diphosphate)

PDB for NP0338638 (syn-Copalyl diphosphate)

3D PDB for NP0338638 (syn-Copalyl diphosphate)

SMILES for NP0338638 (syn-Copalyl diphosphate)

INCHI for NP0338638 (syn-Copalyl diphosphate)

Structure for NP0338638 (syn-Copalyl diphosphate)

3D Structure for NP0338638 (syn-Copalyl diphosphate)