Natural Product: NPC124183

Natural Product IDNPC124183
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (3S,8S)-16,17-Didehydrofalcarindiol
IUPAC Name (3S,8S,9Z)-heptadeca-1,9,16-trien-4,6-diyne-3,8-diol
Synonyms (3S,8S)-16,17-Didehydrofalcarindiol
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL459266
PubChem CID 5469786
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002951] Long-chain fatty alcohols

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey OLUQMFYBNOJBQQ-RCQSYPNMSA-N
Standard InCHI InChI=1S/C17H22O2/c1-3-5-6-7-8-9-10-14-17(19)15-12-11-13-16(18)4-2/h3-4,10,14,16-19H,1-2,5-9H2/b14-10-/t16-,17-/m0/s1
SMILES C=CCCCCC/C=C[C@@H](C#CC#C[C@H](C=C)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   258.16 Volume:   301.713
?
Van der Waals volume.
Dense:   0.856 LogP:   3.454
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.879
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.269
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   8.0 Rigid Bonds:   5.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.399 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.354 Fsp3:   0.412
MCE-18:   2.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.023 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.025
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.754 Promiscuous compounds:   0.076

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.693 MDCK Permeability:   -4.688
Pgp-inhibitor:   0.165 Pgp-substrate:   0.0
PAMPA:   0.971
?
The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
 Human Intestinal Absorption (HIA):   0.0
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.001
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.0
Plasma Protein Binding (PPB):   96.026% Volume Distribution (VD):   -0.13
Fu: 3.522%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.0 BCRP inhibitor:   1.0
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.997
CYP2C19-inhibitor:   0.015 CYP2C19-substrate:   0.081
CYP2C9-inhibitor:   0.996 CYP2C9-substrate:   0.016
CYP2D6-inhibitor:   0.705 CYP2D6-substrate:   0.993
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.36
?
Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  4.373 Half-life (T1/2):  1.543

ADMET: Toxicity

hERG Blockers:  0.023 hERG Blockers (10um):  0.708
Human Hepatotoxicity (H-HT):  0.109 Drug-induced Liver Injury (DILI):  0.122
AMES Toxicity:  0.433 Rat Oral Acute Toxicity:  0.617
Maximum Recommended Daily Dose:  0.68 Skin Sensitization:  0.995
Carcinogencity:  0.383 Eye Corrosion:  1.0
Eye Irritation:  0.999 Respiratory Toxicity:  1.0
Drug-induced Neurotoxicity:  0.276 Ototoxicity:  0.245
Hematotoxicity:  0.004 Drug-induced Nephrotoxicity:  0.011
Genotoxicity:  0.017 RPMI-8226 Immunitoxicity:  0.077
A549 Cytotoxicity:  0.112 Hek293 Cytotoxicity:  0.398
BCF:   1.765
?
Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
 IGC50:   4.394
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.238
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.615
?
96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. PMID[1431947]
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. PMID[1453179]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[17262892]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. fruit n.a. PMID[21163339]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota aerial parts n.a. n.a. PMID[23819871]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[31181918]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[3430163]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37446759]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO21711 Dendropanax arboreus Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[8792622]
NPO21711 Dendropanax arboreus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18448 Hamelia patens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19387 Hazardia squarrosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12902 Alstonia undulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21236 Annona crassiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18448 Hamelia patens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22011 Myrmekioderma styx Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO17123 Delphinium roylei Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13870 Podocarpium podocarpum n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12139 Cylindrotheca closterium Species Bacillariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5406 Veronica chamaedrys Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9385 Glycosmis ovoidea Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14084 Roccella fucoides Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2509 Strombus gigas Species Strombidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14730 Bonnetia dinizii Species Bonnetiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4031.1 Cynara cardunculus var. scolymus Varieties Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7728 Vitex agnus-castus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2090 Baccharis thesioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO368 Dendroaspis angusticeps Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18458 Raukaua simplex Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21369 Paullinia scarlatina Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21711 Dendropanax arboreus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17649 Eugenia caryophyllus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18274 Centaurea deusta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17800 Isodon rosthornii Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18065 Siparuna gilgiana Species Siparunaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19387 Hazardia squarrosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22185 Cocculus indicus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12187 Convolvulus arvensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22300 Soulamea amara Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21236 Annona crassiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19250 Digitalis orientalis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3495 Matsucoccus feytaudi Species Margarodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12902 Alstonia undulata Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. GI50 = 2100.0 nM PMID[8792622]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. TGI = 3000.0 nM PMID[8792622]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 3.0 % PMID[8792622]

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus Activity = 14.5 day PMID[8792622]
NPT32 Organism Mus musculus Mus musculus Activity = 14.0 day PMID[8792622]
NPT32 Organism Mus musculus Mus musculus Activity = 15.5 day PMID[8792622]
NPT32 Organism Mus musculus Mus musculus Activity = 15.0 day PMID[8792622]





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC124183 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
1.0 High Similarity NPC482802
0.8929 High Similarity NPC243813
0.8333 Intermediate Similarity NPC91226
0.8333 Intermediate Similarity NPC243546
0.8333 Intermediate Similarity NPC31194
0.8333 Intermediate Similarity NPC248884
0.7812 Intermediate Similarity NPC153538
0.7812 Intermediate Similarity NPC93639
0.7353 Intermediate Similarity NPC482801
0.7143 Intermediate Similarity NPC142092
0.6944 Remote Similarity NPC35141
0.6765 Remote Similarity NPC321763
0.6765 Remote Similarity NPC101616
0.6471 Remote Similarity NPC72699
0.6471 Remote Similarity NPC481854
0.641 Remote Similarity NPC66460
0.641 Remote Similarity NPC325929
0.641 Remote Similarity NPC271282
0.6098 Remote Similarity NPC212730
0.6 Remote Similarity NPC481860
0.5946 Remote Similarity NPC484320
0.5946 Remote Similarity NPC168510
0.5946 Remote Similarity NPC481848
0.5814 Remote Similarity NPC265551
0.5676 Remote Similarity NPC481855
0.5676 Remote Similarity NPC55063
0.5676 Remote Similarity NPC19834
0.5676 Remote Similarity NPC166942
0.5667 Remote Similarity NPC125122
0.5667 Remote Similarity NPC471276
0.5667 Remote Similarity NPC471280
0.5667 Remote Similarity NPC471281
0.5641 Remote Similarity NPC85079
0.5641 Remote Similarity NPC151782
0.5556 Remote Similarity NPC484322
0.5484 Remote Similarity NPC170776
0.5484 Remote Similarity NPC9273
0.5484 Remote Similarity NPC165447
0.5484 Remote Similarity NPC471959
0.5484 Remote Similarity NPC199286
0.5484 Remote Similarity NPC489046
0.5484 Remote Similarity NPC76198
0.5484 Remote Similarity NPC610719
0.5385 Remote Similarity NPC48821
0.5385 Remote Similarity NPC13418
0.5312 Remote Similarity NPC607242
0.5152 Remote Similarity NPC249670
0.5135 Remote Similarity NPC55383
0.5116 Remote Similarity NPC29697

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC124183 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data