Natural Product: NPC508602

Natural Product IDNPC508602
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (Z)-dec-5-en-1-ol
IUPAC Name dec-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 WYPQHXVMNVEVEB-UHFFFAOYSA-N
Standard InCHI InChI=1S/C10H20O/c1-2-3-4-5-6-7-8-9-10-11/h5-6,11H,2-4,7-10H2,1H3
SMILES CCCCC=CCCCCO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   156.15 Volume:   187.67
?
Van der Waals volume.
Dense:   0.832 LogP:   3.583
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.877
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.026
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The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 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:   0.444 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.173 Fsp3:   0.8
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:   Rejected
Golden Triangle Rule:   Accepted 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:   0.001
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   1.0 Promiscuous compounds:   0.249

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.907 MDCK Permeability:   -4.741
Pgp-inhibitor:   0.469 Pgp-substrate:   0.444
PAMPA:   0.057
?
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):   0.378
20% Bioavailability (F20%):   0.362 30% Bioavailability (F30%):   0.653
50% Bioavailability (F50%):   0.607

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.684 MRP1:   0.743
Plasma Protein Binding (PPB):   89.577% Volume Distribution (VD):   -0.468
Fu: 9.969%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.045
OATP1B3 inhibitor:   0.47 BCRP inhibitor:   0.707
BSEP inhibitor:   0.66

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.414
CYP2C19-inhibitor:   0.848 CYP2C19-substrate:   0.015
CYP2C9-inhibitor:   0.999 CYP2C9-substrate:   0.005
CYP2D6-inhibitor:   0.976 CYP2D6-substrate:   0.896
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.237
CYP2B6-substrate:   0.853 CYP2C8-inhibitor:   0.982
HLM stability:   0.68
?
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):  7.946 Half-life (T1/2):  0.762

ADMET: Toxicity

hERG Blockers:  0.287 hERG Blockers (10um):  0.607
Human Hepatotoxicity (H-HT):  0.161 Drug-induced Liver Injury (DILI):  0.002
AMES Toxicity:  0.155 Rat Oral Acute Toxicity:  0.055
Maximum Recommended Daily Dose:  0.04 Skin Sensitization:  0.999
Carcinogencity:  0.131 Eye Corrosion:  0.999
Eye Irritation:  0.999 Respiratory Toxicity:  0.401
Drug-induced Neurotoxicity:  0.013 Ototoxicity:  0.16
Hematotoxicity:  0.023 Drug-induced Nephrotoxicity:  0.291
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.047
A549 Cytotoxicity:  0.324 Hek293 Cytotoxicity:  0.116
BCF:   1.536
?
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:   3.495
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.576
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.089
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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
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[19245261]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20151678]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20853876]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[35481430]
NPO21300 Zanthoxylum carolinianum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19826 Helicoverpa armigera Species Noctuidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21946 Fissistigma polyanthum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2731 Craterellus tubaeformis Species Cantharellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23078 Coniesta ignefusalis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO21946 Fissistigma polyanthum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29016 Valeriana jatamansi Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21300 Zanthoxylum carolinianum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19826 Helicoverpa armigera Species Noctuidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2731 Craterellus tubaeformis Species Cantharellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23078 Coniesta ignefusalis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO21946 Fissistigma polyanthum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29016 Valeriana jatamansi Species Caprifoliaceae 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 NPC508602 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
0.8 Intermediate Similarity NPC252978
0.7619 Intermediate Similarity NPC76976
0.5789 Remote Similarity NPC275462
0.5556 Remote Similarity NPC52403
0.55 Remote Similarity NPC126915
0.55 Remote Similarity NPC205141
0.55 Remote Similarity NPC24506
0.55 Remote Similarity NPC225783
0.55 Remote Similarity NPC279895
0.55 Remote Similarity NPC185538
0.55 Remote Similarity NPC181516
0.55 Remote Similarity NPC163556
0.55 Remote Similarity NPC139131
0.55 Remote Similarity NPC236797
0.55 Remote Similarity NPC291158
0.55 Remote Similarity NPC272998
0.55 Remote Similarity NPC112242
0.55 Remote Similarity NPC185041
0.55 Remote Similarity NPC147096
0.5294 Remote Similarity NPC294703

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC508602 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
0.55 Remote Similarity NPD2272 Phase 4
0.55 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