NP-MRD: Showing NP-Card for Aphidicolane-3alpha,16,17,18-tetraol (NP0050543)

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Record Information

Version

1.0

Created at

2022-04-27 21:56:23 UTC

Updated at

2022-04-27 21:56:23 UTC

NP-MRD ID

NP0050543

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Aphidicolane-3alpha,16,17,18-tetraol

Description

Aphidicolin belongs to the class of organic compounds known as aphidicolane and stemodane diterpenoids. These are diterpenoids with a structure based on the aphidicolane or the stemodane skeleton. Aphidicolane-3alpha,16,17,18-tetraol is found in Cephalosporium aphidicola, Harziella entomophilla, Nigrospora sphaerica, Phoma betae, Pleospora bjoerlingii and Tolypocladium inflatum. It was first documented in 1992 (PMID: 1483268). Aphidicolin is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 10592317) (PMID: 19735659) (PMID: 21212237) (PMID: 21444690).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 09041213532D          

 28 31  0  0  0  0            999 V2000
    3.9765   -0.2935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9226    1.4553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0962   -0.7441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8914   -0.5140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4783    1.8965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6871    1.6626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4550    1.5683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6519    1.8973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6115   -0.3056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9200    0.6328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7069    0.4755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4197    2.0073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4815   -0.1728    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2078    0.4630    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0924    0.2923    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0764    1.3284    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8835    0.5262    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4942    0.8604    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6461    0.6918    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0261    1.3131    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0747   -0.2630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2437    1.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8676    1.5623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    0.9990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2388   -0.9613    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5680    0.1823    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6882   -0.2783    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2694    2.1305    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 13  3  1  0  0  0  0
 13  9  1  0  0  0  0
 14  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15  4  1  0  0  0  0
 16  5  1  0  0  0  0
 17  1  1  6  0  0  0
 17 11  1  1  0  0  0
 17 15  1  0  0  0  0
 17 16  1  0  0  0  0
 18  2  1  6  0  0  0
 18  6  1  0  0  0  0
 18 15  1  0  0  0  0
 19  7  1  0  0  0  0
 19 10  1  6  0  0  0
 19 13  1  0  0  0  0
 19 18  1  0  0  0  0
 20  8  1  0  0  0  0
 20 12  1  1  0  0  0
 20 14  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 16 23  1  1  0  0  0
 20 24  1  6  0  0  0
 13 25  1  6  0  0  0
 14 26  1  6  0  0  0
 15 27  1  1  0  0  0
 16 28  1  6  0  0  0
M  END


  Mrv0541 09041213532D          

 28 31  0  0  0  0            999 V2000
    3.9765   -0.2935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9226    1.4553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0962   -0.7441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8914   -0.5140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4783    1.8965    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6871    1.6626    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4550    1.5683    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6519    1.8973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6115   -0.3056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9200    0.6328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7069    0.4755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4197    2.0073    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4815   -0.1728    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2078    0.4630    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0924    0.2923    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0764    1.3284    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8835    0.5262    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4942    0.8604    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6461    0.6918    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0261    1.3131    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.0747   -0.2630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2437    1.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8676    1.5623    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    0.9990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2388   -0.9613    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5680    0.1823    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6882   -0.2783    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2694    2.1305    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 13  3  1  0  0  0  0
 13  9  1  0  0  0  0
 14  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15  4  1  0  0  0  0
 16  5  1  0  0  0  0
 17  1  1  6  0  0  0
 17 11  1  1  0  0  0
 17 15  1  0  0  0  0
 17 16  1  0  0  0  0
 18  2  1  6  0  0  0
 18  6  1  0  0  0  0
 18 15  1  0  0  0  0
 19  7  1  0  0  0  0
 19 10  1  6  0  0  0
 19 13  1  0  0  0  0
 19 18  1  0  0  0  0
 20  8  1  0  0  0  0
 20 12  1  1  0  0  0
 20 14  1  0  0  0  0
 21 11  1  0  0  0  0
 22 12  1  0  0  0  0
 16 23  1  1  0  0  0
 20 24  1  6  0  0  0
 13 25  1  6  0  0  0
 14 26  1  6  0  0  0
 15 27  1  1  0  0  0
 16 28  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0050543

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@]3([H])C[C@]1(CC[C@]3(O)CO)[C@@]1(C)CC[C@@]([H])(O)[C@@](C)(CO)[C@]1([H])CC2

> <INCHI_IDENTIFIER>
InChI=1S/C20H34O4/c1-17(11-21)15-4-3-13-9-14-10-19(13,7-8-20(14,24)12-22)18(15,2)6-5-16(17)23/h13-16,21-24H,3-12H2,1-2H3/t13-,14+,15-,16+,17-,18-,19-,20-/m0/s1

> <INCHI_KEY>
NOFOAYPPHIUXJR-APNQCZIXSA-N

> <FORMULA>
C20H34O4

> <MOLECULAR_WEIGHT>
338.4816

> <EXACT_MASS>
338.245709576

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
38.6592401840758

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,5R,6R,7R,10S,12R,13R)-6,13-bis(hydroxymethyl)-2,6-dimethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecane-5,13-diol

> <ALOGPS_LOGP>
1.42

> <JCHEM_LOGP>
1.0900845609999998

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.481420194628729

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.633374063733939

> <JCHEM_PKA_STRONGEST_BASIC>
-2.785448450815384

> <JCHEM_POLAR_SURFACE_AREA>
80.92

> <JCHEM_REFRACTIVITY>
92.38489999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.63e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
aphidicolin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-12         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  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   17                                                            
CONECT    2   18                                                            
CONECT    3    4   13                                                       
CONECT    4    3   15                                                       
CONECT    5    6   16                                                       
CONECT    6    5   18                                                       
CONECT    7    8   19                                                       
CONECT    8    7   20                                                       
CONECT    9   13   14                                                       
CONECT   10   14   19                                                       
CONECT   11   17   21                                                       
CONECT   12   20   22                                                       
CONECT   13    3    9   19   25                                             
CONECT   14    9   10   20   26                                             
CONECT   15    4   17   18   27                                             
CONECT   16    5   17   23   28                                             
CONECT   17    1   11   15   16                                             
CONECT   18    2    6   15   19                                             
CONECT   19    7   10   13   18                                             
CONECT   20    8   12   14   24                                             
CONECT   21   11                                                            
CONECT   22   12                                                            
CONECT   23   16                                                            
CONECT   24   20                                                            
CONECT   25   13                                                            
CONECT   26   14                                                            
CONECT   27   15                                                            
CONECT   28   16                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   62    0
END

View in JSmol

Synonyms

Value	Source
(3alpha,4alpha,5alpha,17alpha)-3,17-Dihydroxy-4-methyl-9,15-cyclo-C,18-dinor-14,15-secoandrostane-4,17-dimethanol	ChEBI
Aphidocolin	ChEBI
(3a,4a,5a,17a)-3,17-Dihydroxy-4-methyl-9,15-cyclo-C,18-dinor-14,15-secoandrostane-4,17-dimethanol	Generator
(3Α,4α,5α,17α)-3,17-dihydroxy-4-methyl-9,15-cyclo-C,18-dinor-14,15-secoandrostane-4,17-dimethanol	Generator
Aphidicolin, (3-S-(3alpha,4beta,4abeta,6aalpha,8alpha,9alpha,11aalpha,11balpha))-isomer	MeSH

Chemical Formula

C₂₀H₃₄O₄

Average Mass

338.4816 Da

Monoisotopic Mass

338.24571 Da

IUPAC Name

(1S,2S,5R,6R,7R,10S,12R,13R)-6,13-bis(hydroxymethyl)-2,6-dimethyltetracyclo[10.3.1.0¹,¹⁰.0²,⁷]hexadecane-5,13-diol

Traditional Name

aphidicolin

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@]3([H])C[C@]1(CC[C@]3(O)CO)[C@@]1(C)CC[C@@]([H])(O)[C@@](C)(CO)[C@]1([H])CC2

InChI Identifier

InChI=1S/C20H34O4/c1-17(11-21)15-4-3-13-9-14-10-19(13,7-8-20(14,24)12-22)18(15,2)6-5-16(17)23/h13-16,21-24H,3-12H2,1-2H3/t13-,14+,15-,16+,17-,18-,19-,20-/m0/s1

InChI Key

NOFOAYPPHIUXJR-APNQCZIXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cephalosporium aphidicola ,	-	KNApSAcK
Harziella entomophilla	-	KNApSAcK
Nigrospora sphaerica	-	KNApSAcK
Phoma betae	LOTUS Database	35616633
Pleospora bjoerlingii	LOTUS Database	35616633
Tolypocladium inflatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aphidicolane and stemodane diterpenoids. These are diterpenoids with a structure based on the aphidicolane or the stemodane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Aphidicolane and stemodane diterpenoids

Alternative Parents

Substituents

Aphidicolane or stemodane diterpenoid
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

tetracyclic diterpenoid (CHEBI:2766 )

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	1.42	ALOGPS
logP	1.09	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	13.63	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	92.38 m³·mol⁻¹	ChemAxon
Polarizability	38.66 Å³	ChemAxon
Number of Rings	4	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

Not Available

KNApSAcK ID

C00023944

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

CPD-11426

BiGG ID

Not Available

Wikipedia Link

Aphidicolin

METLIN ID

Not Available

PubChem Compound

457964

PDB ID

Not Available

ChEBI ID

2766

Good Scents ID

Not Available

References

General References

Carme F, Rosa M, Josep E: Chromosome aberrations induced by aphidicolin. Mutat Res. 1999 Nov 29;430(1):47-53. doi: 10.1016/s0027-5107(99)00125-6. [PubMed:10592317 ]
Cinatl J, Cinatl J, Mainke M, Weissflog A, Steigmann G, Rabenau H, Doerr HW, Kornhuber B: Aphidicolin selectively kills neuroblastoma cells in vitro. Cancer Lett. 1992 Dec 24;67(2-3):199-206. doi: 10.1016/0304-3835(92)90144-k. [PubMed:1483268 ]
Hofstetrova K, Uzlikova M, Tumova P, Troell K, Svard SG, Nohynkova E: Giardia intestinalis: aphidicolin influence on the trophozoite cell cycle. Exp Parasitol. 2010 Feb;124(2):159-66. doi: 10.1016/j.exppara.2009.09.004. Epub 2009 Sep 6. [PubMed:19735659 ]
Arlt MF, Ozdemir AC, Birkeland SR, Lyons RH Jr, Glover TW, Wilson TE: Comparison of constitutional and replication stress-induced genome structural variation by SNP array and mate-pair sequencing. Genetics. 2011 Mar;187(3):675-83. doi: 10.1534/genetics.110.124776. Epub 2011 Jan 6. [PubMed:21212237 ]
Harrigan JA, Belotserkovskaya R, Coates J, Dimitrova DS, Polo SE, Bradshaw CR, Fraser P, Jackson SP: Replication stress induces 53BP1-containing OPT domains in G1 cells. J Cell Biol. 2011 Apr 4;193(1):97-108. doi: 10.1083/jcb.201011083. Epub 2011 Mar 28. [PubMed:21444690 ]

Showing NP-Card for Aphidicolane-3alpha,16,17,18-tetraol (NP0050543)

MOL for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

3D MOL for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

3D SDF for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

3D-SDF for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

PDB for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

3D PDB for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

SMILES for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

INCHI for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

Structure for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)

3D Structure for NP0050543 (Aphidicolane-3alpha,16,17,18-tetraol)