Natural Product: NPC596737

Natural Product IDNPC596737
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Tetradec-5-en-1-ol
IUPAC Name tetradec-5-en-1-ol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 ZYTGEAXLNDKCTI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H28O/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15/h9-10,15H,2-8,11-14H2,1H3
SMILES CCCCCCCCC=CCCCCO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   212.21 Volume:   256.854
?
Van der Waals volume.
Dense:   0.826 LogP:   5.178
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.437
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.57
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   1.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.396 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.056 Fsp3:   0.857
MCE-18:   0.0
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.022 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.3

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.028 MDCK Permeability:   -4.76
Pgp-inhibitor:   0.115 Pgp-substrate:   0.255
PAMPA:   0.007
?
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):   0.838
20% Bioavailability (F20%):   0.672 30% Bioavailability (F30%):   0.923
50% Bioavailability (F50%):   0.717

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.258 MRP1:   0.876
Plasma Protein Binding (PPB):   97.72% Volume Distribution (VD):   -0.022
Fu: 2.198%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.057
OATP1B3 inhibitor:   0.984 BCRP inhibitor:   0.797
BSEP inhibitor:   0.766

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.998
CYP2C19-inhibitor:   0.003 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.003
CYP2D6-inhibitor:   0.995 CYP2D6-substrate:   0.409
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.11 CYP2C8-inhibitor:   0.993
HLM stability:   0.023
?
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):  6.177 Half-life (T1/2):  0.399

ADMET: Toxicity

hERG Blockers:  0.331 hERG Blockers (10um):  0.639
Human Hepatotoxicity (H-HT):  0.256 Drug-induced Liver Injury (DILI):  0.005
AMES Toxicity:  0.146 Rat Oral Acute Toxicity:  0.07
Maximum Recommended Daily Dose:  0.065 Skin Sensitization:  0.999
Carcinogencity:  0.169 Eye Corrosion:  0.999
Eye Irritation:  0.999 Respiratory Toxicity:  0.641
Drug-induced Neurotoxicity:  0.011 Ototoxicity:  0.164
Hematotoxicity:  0.031 Drug-induced Nephrotoxicity:  0.313
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.043
A549 Cytotoxicity:  0.475 Hek293 Cytotoxicity:  0.163
BCF:   2.377
?
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:   4.868
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.575
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.214
?
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
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[10075766]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[11112781]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[153409]
NPO658 Leucopaxillus gentianeus Species Tricholomataceae Eukaryota n.a. n.a. n.a. PMID[15568769]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO658 Leucopaxillus gentianeus Species Tricholomataceae Eukaryota fruiting bodies n.a. n.a. PMID[17190463]
NPO28092 Xyris pterygoblephara Species Xyridaceae Eukaryota n.a. n.a. n.a. PMID[17870137]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. stem n.a. PMID[18239317]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. root n.a. PMID[18239317]
NPO28092 Xyris pterygoblephara Species Xyridaceae Eukaryota n.a. n.a. n.a. PMID[18462007]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[21673922]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23265519]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23317005]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[23488669]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[27524650]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[29115831]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. PMID[31182315]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. PMID[31287310]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO6259 Keiferia lycopersicella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7347 Viguiera oblongifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8492 Viburnum urceolatum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10613 Thalictrum longistylum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12081 Streptomyces xanthochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO11709 Salvia parryi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5723 Quercus robur Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7050 Picea mariana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1038 Phoenix loureiroi Species Arecaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13002 Petasites georgicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12677 Penicillium kapuscinskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12317 Naja kaouthia Species Elapidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO658 Leucopaxillus gentianeus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9930 Dendrodoris tuberculosa Species Dendrodorididae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11949 Iris ensata Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4544 Gomortega keule Species Gomortegaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8777 Euryops algoensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12893 Dermolepida albohirtum Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8808 Artemisia schimperi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11558 Atylosia trinervia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28092 Xyris pterygoblephara Species Xyridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27848 Conoideocrella luteorostrata Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. Database[FooDB]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5723 Quercus robur Species Fagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10613 Thalictrum longistylum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5723 Quercus robur Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4544 Gomortega keule Species Gomortegaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO658 Leucopaxillus gentianeus Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12893 Dermolepida albohirtum Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12081 Streptomyces xanthochromogenes Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO21679 Nuphar lutea Species Nymphaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1038 Phoenix loureiroi Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6259 Keiferia lycopersicella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12677 Penicillium kapuscinskii Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9930 Dendrodoris tuberculosa Species Dendrodorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27848 Conoideocrella luteorostrata Species Clavicipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8492 Viburnum urceolatum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO963 Litsea pungens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4240 Elephantopus tomentosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11709 Salvia parryi Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28092 Xyris pterygoblephara Species Xyridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8777 Euryops algoensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5723 Quercus robur Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11949 Iris ensata Species Iridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7050 Picea mariana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13002 Petasites georgicus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7347 Viguiera oblongifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11558 Atylosia trinervia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20523 Bacillus subtilis Species Bacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12317 Naja kaouthia Species Elapidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19984 Turpinia ternata Species Staphyleaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10613 Thalictrum longistylum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8808 Artemisia schimperi Species Asteraceae 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

In vivo activity

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





 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 NPC596737 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
0.9048 High Similarity NPC76976
0.8571 High Similarity NPC252978
0.65 Remote Similarity NPC151719
0.619 Remote Similarity NPC126915
0.619 Remote Similarity NPC205141
0.619 Remote Similarity NPC24506
0.619 Remote Similarity NPC225783
0.619 Remote Similarity NPC279895
0.619 Remote Similarity NPC185538
0.619 Remote Similarity NPC181516
0.619 Remote Similarity NPC163556
0.619 Remote Similarity NPC139131
0.619 Remote Similarity NPC236797
0.619 Remote Similarity NPC291158
0.619 Remote Similarity NPC272998
0.619 Remote Similarity NPC112242
0.619 Remote Similarity NPC185041
0.619 Remote Similarity NPC147096
0.5714 Remote Similarity NPC275462
0.5625 Remote Similarity NPC108195
0.5556 Remote Similarity NPC15934
0.5172 Remote Similarity NPC474642
0.5172 Remote Similarity NPC473913
0.5161 Remote Similarity NPC47333

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC596737 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
0.619 Remote Similarity NPD2272 Phase 4
0.619 Remote Similarity NPD5383 Phase 4

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