MiMeDB: Showing metabocard for Atpenin A4 (MMDBc0009476)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:58:30 UTC

Update Date

2025-10-07 16:05:36 UTC

Metabolite ID

MMDBc0009476

Metabolite Identification

Common Name

Atpenin A4

Description

Atpenin A4 is a pyridine derivative belonging to the class of natural products known as alkaloids. This compound has garnered attention due to its biological activity, particularly its ability to inhibit the growth of human prostate cancer DU-145 cells in coculture with human prostate stromal cells, demonstrating a stronger effect than in monoculture (PMID:19282876 ). The molecular structure of atpenin A4 has been elucidated through single crystal X-ray crystallographic analysis, confirming its absolute configuration as 2'S,4'S,5'S-5,6-dimethoxy-4-hydroxy-5'-chloro-2',4'-dimethyl-1'-oxoheptyl-2-hydroxypyridine (I') (PMID:2276974 ). These findings highlight the potential of atpenin A4 as a candidate for further investigation in cancer therapeutics, given its structural complexity and promising biological effects.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103582D          

 25 25  0  0  1  0            999 V2000
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  1  0  0  0
  7  6  1  0  0  0  0
  8  2  1  6  0  0  0
  8  6  1  0  0  0  0
  9  3  1  0  0  0  0
  9  7  1  0  0  0  0
 11  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12 10  2  0  0  0  0
 13 12  1  0  0  0  0
 14 10  1  0  0  0  0
 15 13  2  0  0  0  0
  9 16  1  6  0  0  0
 17 14  2  0  0  0  0
 17 15  1  0  0  0  0
 18 11  2  0  0  0  0
 19 12  1  0  0  0  0
 20 14  1  0  0  0  0
 21  4  1  0  0  0  0
 21 13  1  0  0  0  0
 22  5  1  0  0  0  0
 22 15  1  0  0  0  0
  7 23  1  6  0  0  0
  8 24  1  1  0  0  0
  9 25  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009476

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(C[C@]([H])(C)[C@]([H])(C)Cl)C(=O)C1=C(O)C(OC)=C(OC)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22ClNO5/c1-7(9(3)16)6-8(2)11(18)10-12(19)13(21-4)15(22-5)17-14(10)20/h7-9H,6H2,1-5H3,(H2,17,19,20)/t7-,8-,9-/m0/s1

> <INCHI_KEY>
LDPADGWFJFHTLH-CIUDSAMLSA-N

> <FORMULA>
C15H22ClNO5

> <MOLECULAR_WEIGHT>
331.79

> <EXACT_MASS>
331.1186505

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
32.634588687286865

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,4S,5S)-5-chloro-1-(2,4-dihydroxy-5,6-dimethoxypyridin-3-yl)-2,4-dimethylhexan-1-one

> <ALOGPS_LOGP>
3.17

> <JCHEM_LOGP>
4.711783338666667

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.349807587840399

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.433675155280415

> <JCHEM_PKA_STRONGEST_BASIC>
-0.653272192237844

> <JCHEM_POLAR_SURFACE_AREA>
88.88000000000001

> <JCHEM_REFRACTIVITY>
84.0926

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.94e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4S,5S)-5-chloro-1-(2,4-dihydroxy-5,6-dimethoxypyridin-3-yl)-2,4-dimethylhexan-1-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -8.002   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.668  -0.770   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      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   16 Cl   UNK     0      -6.668  -2.310   0.000  0.00  0.00          Cl+0
HETATM   17  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0      -4.001   0.770   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -6.668   0.770   0.000  0.00  0.00           H+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    9                                                            
CONECT    4   21                                                            
CONECT    5   22                                                            
CONECT    6    7    8                                                       
CONECT    7    1    6    9   23                                             
CONECT    8    2    6   11   24                                             
CONECT    9    3    7   16   25                                             
CONECT   10   11   12   14                                                  
CONECT   11    8   10   18                                                  
CONECT   12   10   13   19                                                  
CONECT   13   12   15   21                                                  
CONECT   14   10   17   20                                                  
CONECT   15   13   17   22                                                  
CONECT   16    9                                                            
CONECT   17   14   15                                                       
CONECT   18   11                                                            
CONECT   19   12                                                            
CONECT   20   14                                                            
CONECT   21    4   13                                                       
CONECT   22    5   15                                                       
CONECT   23    7                                                            
CONECT   24    8                                                            
CONECT   25    9                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₅H₂₂ClNO₅

Average Mass

331.79

Monoisotopic Mass

331.1186505

IUPAC Name

(2S,4S,5S)-5-chloro-1-(2,4-dihydroxy-5,6-dimethoxypyridin-3-yl)-2,4-dimethylhexan-1-one

Traditional Name

(2S,4S,5S)-5-chloro-1-(2,4-dihydroxy-5,6-dimethoxypyridin-3-yl)-2,4-dimethylhexan-1-one

CAS Registry Number

Not Available

SMILES

[H][C@](C)(C[C@]([H])(C)[C@]([H])(C)Cl)C(=O)C1=C(O)C(OC)=C(OC)N=C1O

InChI Identifier

InChI=1S/C15H22ClNO5/c1-7(9(3)16)6-8(2)11(18)10-12(19)13(21-4)15(22-5)17-14(10)20/h7-9H,6H2,1-5H3,(H2,17,19,20)/t7-,8-,9-/m0/s1

InChI Key

LDPADGWFJFHTLH-CIUDSAMLSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aryl alkyl ketones. These are ketones have the generic structure RC(=O)R', where R = aryl group and R'=alkyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Aryl alkyl ketones

Alternative Parents

Substituents

Aryl alkyl ketone
Alkyl aryl ether
Dihydropyridine
Hydroxypyridine
Pyridinone
Hydropyridine
Pyridine
Heteroaromatic compound
Vinylogous amide
Vinylogous acid
Lactam
Ether
Azacycle
Organoheterocyclic compound
Organohalogen compound
Alkyl chloride
Hydrocarbon derivative
Organic nitrogen compound
Organic oxide
Organochloride
Organonitrogen compound
Alkyl halide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.39 g/L	ALOGPS
logP	3.17	ALOGPS
logP	4.71	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	10.43	ChemAxon
pKa (Strongest Basic)	-0.65	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	88.88 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	84.09 m³·mol⁻¹	ChemAxon
Polarizability	32.63 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

170827

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

197274

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Atpenin A4 (MMDBc0009476)

MOL for #<Metabolite:0x00007f2ac46983e0>

3D MOL for #<Metabolite:0x00007f2ac46983e0>

3D SDF for #<Metabolite:0x00007f2ac46983e0>

3D-SDF for #<Metabolite:0x00007f2ac46983e0>

PDB for #<Metabolite:0x00007f2ac46983e0>

3D PDB for #<Metabolite:0x00007f2ac46983e0>

SMILES for #<Metabolite:0x00007f2ac46983e0>

INCHI for #<Metabolite:0x00007f2ac46983e0>

Structure for #<Metabolite:0x00007f2ac46983e0>

3D Structure for #<Metabolite:0x00007f2ac46983e0>