Natural Product: NPC553814

Natural Product IDNPC553814
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 2,6,11-trimethyl-dodeca-2,6,10-triene
IUPAC Name 2,6,11-trimethyldodeca-2,6,10-triene
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 SATOEJVASOISEY-UHFFFAOYSA-N
Standard InCHI InChI=1S/C15H26/c1-13(2)9-6-7-11-15(5)12-8-10-14(3)4/h9-11H,6-8,12H2,1-5H3
SMILES CC(C)=CCCC=C(C)CCC=C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   206.2 Volume:   260.087
?
Van der Waals volume.
Dense:   0.793 LogP:   6.293
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.918
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.238
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   3.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.402 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.735 Fsp3:   0.6
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:   0.087 Fluc inhibitor:   0.029
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.004
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.999 Promiscuous compounds:   0.105

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.538 MDCK Permeability:   -4.749
Pgp-inhibitor:   0.962 Pgp-substrate:   0.096
PAMPA:   0.048
?
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):   0.007
20% Bioavailability (F20%):   0.022 30% Bioavailability (F30%):   0.02
50% Bioavailability (F50%):   0.612

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.827 MRP1:   0.958
Plasma Protein Binding (PPB):   96.395% Volume Distribution (VD):   0.119
Fu: 4.544%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.968
OATP1B3 inhibitor:   0.854 BCRP inhibitor:   0.175
BSEP inhibitor:   0.894

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.222
CYP2C19-inhibitor:   0.99 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.274 CYP2C9-substrate:   0.008
CYP2D6-inhibitor:   0.656 CYP2D6-substrate:   0.056
CYP3A4-inhibitor:   0.004 CYP3A4-substrate:   0.927
CYP2B6-substrate:   0.012 CYP2C8-inhibitor:   0.022
HLM stability:   0.785
?
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):  11.198 Half-life (T1/2):  0.971

ADMET: Toxicity

hERG Blockers:  0.068 hERG Blockers (10um):  0.504
Human Hepatotoxicity (H-HT):  0.475 Drug-induced Liver Injury (DILI):  0.079
AMES Toxicity:  0.071 Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.046 Skin Sensitization:  0.996
Carcinogencity:  0.363 Eye Corrosion:  0.997
Eye Irritation:  0.998 Respiratory Toxicity:  0.701
Drug-induced Neurotoxicity:  0.683 Ototoxicity:  0.253
Hematotoxicity:  0.331 Drug-induced Nephrotoxicity:  0.216
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.042
A549 Cytotoxicity:  0.082 Hek293 Cytotoxicity:  0.02
BCF:   2.574
?
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:   5.039
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.065
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.42
?
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
NPO4331 Plakortis lita Species Plakinidae Eukaryota n.a. Palauan n.a. PMID[10479343]
NPO4331 Plakortis lita Species Plakinidae Eukaryota n.a. Okinawan n.a. PMID[11277756]
NPO25126 Sarcophyton latum Species Orchidaceae Eukaryota n.a. Hainan soft coral n.a. PMID[16724849]
NPO25126 Sarcophyton latum Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[16724849]
NPO4435 Brunfelsia grandiflora Species Solanaceae Eukaryota n.a. leaf n.a. PMID[18175984]
NPO8247 Austrobaileya scandens Species Austrobaileyaceae Eukaryota n.a. n.a. n.a. PMID[27214307]
NPO2861 Pentaceraster regulus Species n.a. n.a. n.a. n.a. n.a. PMID[28981263]
NPO4435 Brunfelsia grandiflora Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[36235047]
NPO4331 Plakortis lita Species Plakinidae Eukaryota n.a. n.a. n.a. PMID[9722494]
NPO14349 Aconitum turczaninowii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1462 Amomum sulcatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24257 Asphodeline lutea Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4435 Brunfelsia grandiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14496 Eranthis cilicica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14099 Ocotea pretiosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO48808 Prosuberites laughlini Species Suberitidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12837 Simsia dombeyana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20177 Verbesina luetzelburgii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25126 Sarcophyton latum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6791 Malva rotundifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27884 Sphacelaria arctica Species Sphacelariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5844 Schlumbergera truncata Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4888 Salvia divaricata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO345 Quercus laurifolia Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4331 Plakortis lita Species Plakinidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2861 Pentaceraster regulus Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO9215 Papaver glaucum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO569 Micromelum integerrimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6053 Veronica intercedens Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5582 Inocybe aeruginascens Species Inocybaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3331 Hedysarum sachalinense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6305 Euphorbia jaxartica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7401 Centaurea dealbata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO134 Cassia artemisioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO772 Bosistoa floydii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8247 Austrobaileya scandens Species Austrobaileyaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO569 Micromelum integerrimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5844 Schlumbergera truncata Species Cactaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO569 Micromelum integerrimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO569 Micromelum integerrimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO6305 Euphorbia jaxartica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3331 Hedysarum sachalinense Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6791 Malva rotundifolia Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14496 Eranthis cilicica Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5844 Schlumbergera truncata Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO345 Quercus laurifolia Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4331 Plakortis lita Species Plakinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2861 Pentaceraster regulus Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4888 Salvia divaricata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27884 Sphacelaria arctica Species Sphacelariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9215 Papaver glaucum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1462 Amomum sulcatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5582 Inocybe aeruginascens Species Inocybaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO134 Cassia artemisioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7401 Centaurea dealbata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO569 Micromelum integerrimum Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12837 Simsia dombeyana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24257 Asphodeline lutea Species Xanthorrhoeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8247 Austrobaileya scandens Species Austrobaileyaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25126 Sarcophyton latum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4435 Brunfelsia grandiflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6053 Veronica intercedens Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO772 Bosistoa floydii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14349 Aconitum turczaninowii Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14099 Ocotea pretiosa Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20177 Verbesina luetzelburgii 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 NPC553814 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 NPC123965
1.0 High Similarity NPC115959
0.7143 Intermediate Similarity NPC305759
0.6522 Remote Similarity NPC29091
0.6522 Remote Similarity NPC185839
0.6522 Remote Similarity NPC103213
0.6522 Remote Similarity NPC300623
0.6522 Remote Similarity NPC213538
0.6522 Remote Similarity NPC269823
0.6522 Remote Similarity NPC39222
0.6522 Remote Similarity NPC9860
0.6522 Remote Similarity NPC180840
0.6087 Remote Similarity NPC160628
0.6 Remote Similarity NPC128280
0.5833 Remote Similarity NPC60288
0.5769 Remote Similarity NPC67761
0.5769 Remote Similarity NPC209279
0.5769 Remote Similarity NPC194586
0.5769 Remote Similarity NPC108494
0.5769 Remote Similarity NPC51758
0.5652 Remote Similarity NPC12319
0.5652 Remote Similarity NPC18205
0.5652 Remote Similarity NPC182840
0.5652 Remote Similarity NPC255042
0.5652 Remote Similarity NPC13217
0.5417 Remote Similarity NPC100879
0.5417 Remote Similarity NPC471327
0.5385 Remote Similarity NPC281590
0.5385 Remote Similarity NPC605369
0.5357 Remote Similarity NPC140501
0.5238 Remote Similarity NPC138113
0.52 Remote Similarity NPC270706
0.5172 Remote Similarity NPC197467
0.5172 Remote Similarity NPC6963
0.5172 Remote Similarity NPC308331

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC553814 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
0.6522 Remote Similarity NPD5783 Phase 3
0.5357 Remote Similarity NPD4265 Phase 2

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