MiMeDB: Showing metabocard for Deoxy-PF1140 (MMDBc0009299)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 01:51:51 UTC

Update Date

2025-10-07 16:05:35 UTC

Metabolite ID

MMDBc0009299

Metabolite Identification

Common Name

Deoxy-PF1140

Description

Deoxy-PF1140 is a tricyclic pyridin-2-one, classified as a metabolite within the chemical class of pyridinones. This compound has garnered attention in the context of its antibacterial activity, particularly against Acinetobacter baumannii, a pathogen known for its multidrug resistance. In a study, deoxy-PF1140 demonstrated a minimum inhibitory concentration (MIC) of 50 μg/mL, indicating its potential as a therapeutic agent against this challenging bacterium (PMID:39887489 ). The structural features of tricyclic pyridin-2-ones, including their ability to interact with bacterial targets, may contribute to their efficacy. Further investigation into the biological mechanisms of deoxy-PF1140 could elucidate its role in antimicrobial resistance and pave the way for the development of novel treatments. Overall, deoxy-PF1140 represents a promising candidate for further research in the field of medicinal chemistry and infectious disease.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152103512D          

 23 25  0  0  1  0            999 V2000
   -0.2211   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.6039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3164   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8414   -1.5395    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2539    0.6039    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4914   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.4914   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.1105    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3164   -1.5395    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0789    0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1914   -0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -1.5395    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  2  0  0  0  0
  9  1  1  1  0  0  0
  9  7  1  0  0  0  0
  9  8  1  0  0  0  0
 10  2  1  1  0  0  0
 10  7  1  0  0  0  0
 11  3  1  6  0  0  0
 12  5  1  0  0  0  0
 13 12  2  0  0  0  0
 14 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15 13  1  0  0  0  0
 16  4  1  1  0  0  0
 16  8  1  0  0  0  0
 16 11  1  0  0  0  0
 16 14  1  0  0  0  0
 17  6  1  0  0  0  0
 17 15  2  0  0  0  0
 18 15  1  0  0  0  0
 19 11  1  0  0  0  0
 19 12  1  0  0  0  0
  9 20  1  6  0  0  0
 10 21  1  6  0  0  0
 11 22  1  6  0  0  0
 14 23  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009299

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(C)C[C@]([H])(C)[C@@]2([H])C3=C(O[C@]([H])(C)[C@@]2(C)C1)C=CN=C3O

> <INCHI_IDENTIFIER>
InChI=1S/C16H23NO2/c1-9-7-10(2)14-13-12(5-6-17-15(13)18)19-11(3)16(14,4)8-9/h5-6,9-11,14H,7-8H2,1-4H3,(H,17,18)/t9-,10+,11-,14+,16-/m1/s1

> <INCHI_KEY>
ZAIJLHHXEHKKNH-LRXDAGSUSA-N

> <FORMULA>
C16H23NO2

> <MOLECULAR_WEIGHT>
261.365

> <EXACT_MASS>
261.172878985

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
29.21550016973983

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R,6aS,8R,10S,10aR)-6,6a,8,10-tetramethyl-6H,6aH,7H,8H,9H,10H,10aH-isochromeno[4,3-c]pyridin-1-ol

> <ALOGPS_LOGP>
4.28

> <JCHEM_LOGP>
3.819268920333334

> <ALOGPS_LOGS>
-3.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.739747024169036

> <JCHEM_PKA_STRONGEST_BASIC>
1.5485772890262364

> <JCHEM_POLAR_SURFACE_AREA>
42.35000000000001

> <JCHEM_REFRACTIVITY>
74.90340000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.56e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6R,6aS,8R,10S,10aR)-6,6a,8,10-tetramethyl-6H,7H,8H,9H,10H,10aH-isochromeno[4,3-c]pyridin-1-ol

> <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      -0.413  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.207  -4.207   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.437   2.461   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.127   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.057  -0.206   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.827  -1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.897  -2.874   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.897  -0.206   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.127  -1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.437  -2.874   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.207   1.127   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.517  -0.206   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.747  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.207  -1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.517  -2.874   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.437  -0.206   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       8.057  -2.874   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       5.747  -4.207   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       5.747   1.127   0.000  0.00  0.00           O+0
HETATM   20  H   UNK     0       0.357  -0.206   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       4.977  -2.874   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       4.977  -0.206   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       2.667  -1.540   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   16                                                            
CONECT    5    6   12                                                       
CONECT    6    5   17                                                       
CONECT    7    9   10                                                       
CONECT    8    9   16                                                       
CONECT    9    1    7    8   20                                             
CONECT   10    2    7   14   21                                             
CONECT   11    3   16   19   22                                             
CONECT   12    5   13   19                                                  
CONECT   13   12   14   15                                                  
CONECT   14   10   13   16   23                                             
CONECT   15   13   17   18                                                  
CONECT   16    4    8   11   14                                             
CONECT   17    6   15                                                       
CONECT   18   15                                                            
CONECT   19   11   12                                                       
CONECT   20    9                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   14                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

Synonyms

Not Available

Molecular Formula

C₁₆H₂₃NO₂

Average Mass

261.365

Monoisotopic Mass

261.172878985

IUPAC Name

(6R,6aS,8R,10S,10aR)-6,6a,8,10-tetramethyl-6H,6aH,7H,8H,9H,10H,10aH-isochromeno[4,3-c]pyridin-1-ol

Traditional Name

(6R,6aS,8R,10S,10aR)-6,6a,8,10-tetramethyl-6H,7H,8H,9H,10H,10aH-isochromeno[4,3-c]pyridin-1-ol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)C[C@]([H])(C)[C@@]2([H])C3=C(O[C@]([H])(C)[C@@]2(C)C1)C=CN=C3O

InChI Identifier

InChI=1S/C16H23NO2/c1-9-7-10(2)14-13-12(5-6-17-15(13)18)19-11(3)16(14,4)8-9/h5-6,9-11,14H,7-8H2,1-4H3,(H,17,18)/t9-,10+,11-,14+,16-/m1/s1

InChI Key

ZAIJLHHXEHKKNH-LRXDAGSUSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as chromenopyridines. These are aromatic heterocyclic compounds structurally characterized by a pyridine ring fused to a chromene moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Chromenopyridines

Alternative Parents

Substituents

Chromenopyridine
Pyranopyridine
Alkyl aryl ether
Pyridinone
Pyridine
Vinylogous ester
Heteroaromatic compound
Lactam
Azacycle
Ether
Oxacycle
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.26 g/L	ALOGPS
logP	4.28	ALOGPS
logP	3.82	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	11.74	ChemAxon
pKa (Strongest Basic)	1.55	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	42.35 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	74.9 m³·mol⁻¹	ChemAxon
Polarizability	29.22 Å³	ChemAxon
Number of Rings	3	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

9440490

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11265479

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 Deoxy-PF1140 (MMDBc0009299)

MOL for #<Metabolite:0x0000564fa0357e60>

3D MOL for #<Metabolite:0x0000564fa0357e60>

3D SDF for #<Metabolite:0x0000564fa0357e60>

3D-SDF for #<Metabolite:0x0000564fa0357e60>

PDB for #<Metabolite:0x0000564fa0357e60>

3D PDB for #<Metabolite:0x0000564fa0357e60>

SMILES for #<Metabolite:0x0000564fa0357e60>

INCHI for #<Metabolite:0x0000564fa0357e60>

Structure for #<Metabolite:0x0000564fa0357e60>

3D Structure for #<Metabolite:0x0000564fa0357e60>