Natural Product: NPC154599

Natural Product IDNPC154599
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XDSYKASBVOZOAG-JYBIWHBTSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12314280
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

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 XDSYKASBVOZOAG-JYBIWHBTSA-N
Standard InCHI InChI=1S/C20H32/c1-6-19(4)13-10-16-15(14-19)8-9-17-18(2,3)11-7-12-20(16,17)5/h6,14,16-17H,1,7-13H2,2-5H3/t16-,17-,19+,20+/m1/s1
SMILES C=C[C@@]1(C)CC[C@@H]2C(=C1)CC[C@@H]1C(C)(C)CCC[C@@]21C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   272.25 Volume:   323.534
?
Van der Waals volume.
Dense:   0.841 LogP:   5.97
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.343
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.724
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.503 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.247 Fsp3:   0.8
MCE-18:   56.0
?
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:   0.611 Fluc inhibitor:   0.061
?
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:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.986 Promiscuous compounds:   0.226

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.618 MDCK Permeability:   -4.793
Pgp-inhibitor:   0.999 Pgp-substrate:   0.0
PAMPA:   0.015
?
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%):   0.248 30% Bioavailability (F30%):   0.588
50% Bioavailability (F50%):   0.905

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.215 MRP1:   0.819
Plasma Protein Binding (PPB):   98.652% Volume Distribution (VD):   0.565
Fu: 1.321%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.994 BCRP inhibitor:   0.7
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.984 CYP1A2-substrate:   0.839
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.312
CYP2C9-inhibitor:   0.826 CYP2C9-substrate:   0.029
CYP2D6-inhibitor:   0.782 CYP2D6-substrate:   0.093
CYP3A4-inhibitor:   0.997 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.046 CYP2C8-inhibitor:   0.997
HLM stability:   0.909
?
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):  10.422 Half-life (T1/2):  0.573

ADMET: Toxicity

hERG Blockers:  0.087 hERG Blockers (10um):  0.449
Human Hepatotoxicity (H-HT):  0.571 Drug-induced Liver Injury (DILI):  0.357
AMES Toxicity:  0.357 Rat Oral Acute Toxicity:  0.344
Maximum Recommended Daily Dose:  0.513 Skin Sensitization:  0.911
Carcinogencity:  0.836 Eye Corrosion:  0.98
Eye Irritation:  0.995 Respiratory Toxicity:  0.925
Drug-induced Neurotoxicity:  0.33 Ototoxicity:  0.248
Hematotoxicity:  0.309 Drug-induced Nephrotoxicity:  0.309
Genotoxicity:  0.146 RPMI-8226 Immunitoxicity:  0.044
A549 Cytotoxicity:  0.21 Hek293 Cytotoxicity:  0.292
BCF:   3.243
?
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:   4.875
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.351
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.755
?
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
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[19673515]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[20536188]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota fruits n.a. n.a. PMID[23265871]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. PMID[8691217]
NPO21101 Felicia amelloides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11064 Haemanthus toxicarius Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20015 Echinocystis lobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22599 Crataegus pontica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28627.1 Coptis trifolia subsp. groenlandica Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18684 Calophyllum thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22529 Calceolaria thyrsiflora Species Calceolariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21822 Berberis crataegina Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16711 Baccharis solieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22711 Athanasia dregeana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22871 Aster alpinus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21530 Arnica viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22812 Acacia cambagei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22927 Xanthoparmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21368 Tricholoma batschii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23025 Roccellaria mollis Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20592 Rhodoglossum japonicum Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23353 [polyangium] brachysporum Species n.a. Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23952 Phlomoides medicinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21951 Paramignya griffithii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28078 Melaleuca decora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22650 Helenium quadridentatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Tubers n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22812 Acacia cambagei Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22927 Xanthoparmelia pokornyi Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23025 Roccellaria mollis Species Roccellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28627.1 Coptis trifolia subsp. groenlandica Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21530 Arnica viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22711 Athanasia dregeana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15478 Senna sophera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20288 Polytolypa hystricis Species Onygenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21582 Manihot esculenta Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28078 Melaleuca decora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20592 Rhodoglossum japonicum Species Gigartinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22871 Aster alpinus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21951 Paramignya griffithii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16711 Baccharis solieri Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19139 Senecio polyodon Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22599 Crataegus pontica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23952 Phlomoides medicinalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8584 Schisandra arisanensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21368 Tricholoma batschii Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23353 [polyangium] brachysporum Species n.a. Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22529 Calceolaria thyrsiflora Species Calceolariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20846 Sophora japonica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20015 Echinocystis lobata Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22294 Pteris inaequalis Species Pteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22650 Helenium quadridentatum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21822 Berberis crataegina Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8198 Podocarpus montanus Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18684 Calophyllum thwaitesii Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11064 Haemanthus toxicarius Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21101 Felicia amelloides 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 NPC154599 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 NPC170070
0.6522 Remote Similarity NPC166797
0.6364 Remote Similarity NPC184918
0.6 Remote Similarity NPC202118
0.6 Remote Similarity NPC145498
0.5778 Remote Similarity NPC478495
0.5745 Remote Similarity NPC91858
0.5652 Remote Similarity NPC149118
0.5652 Remote Similarity NPC241934
0.551 Remote Similarity NPC16345
0.5208 Remote Similarity NPC33303
0.5128 Remote Similarity NPC103290
0.5098 Remote Similarity NPC161923
0.5098 Remote Similarity NPC183503
0.5098 Remote Similarity NPC283908
0.5098 Remote Similarity NPC103958
0.5098 Remote Similarity NPC610917

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC154599 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