Natural Product: NPC155129

Natural Product IDNPC155129
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 LZBXPXAOYQVZEC-RIYZIHGNSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5316534
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids
          • [CHEMONTID:0000051] Aromatic monoterpenoids

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 LZBXPXAOYQVZEC-RIYZIHGNSA-N
Standard InCHI InChI=1S/C15H22O/c1-13(2)6-4-7-14(3)8-5-9-15-10-11-16-12-15/h6,8,10-12H,4-5,7,9H2,1-3H3/b14-8+
SMILES CC(=CCC/C(=C/CCc1ccoc1)/C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   218.17 Volume:   257.684
?
Van der Waals volume.
Dense:   0.847 LogP:   5.662
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.706
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.595
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   7.0
TPSA:   13.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   0.0 Rings:   1.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.619 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.76 Fsp3:   0.467
MCE-18:   6.0
?
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:   0.35 Fluc inhibitor:   0.14
?
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:   0.005
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.994 Promiscuous compounds:   0.008

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.632 MDCK Permeability:   -4.661
Pgp-inhibitor:   0.999 Pgp-substrate:   0.053
PAMPA:   0.006
?
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):   0.031
20% Bioavailability (F20%):   0.044 30% Bioavailability (F30%):   0.047
50% Bioavailability (F50%):   0.526

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.018 MRP1:   0.844
Plasma Protein Binding (PPB):   97.375% Volume Distribution (VD):   0.051
Fu: 2.416%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.758 BCRP inhibitor:   0.034
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.184 CYP1A2-substrate:   0.891
CYP2C19-inhibitor:   0.964 CYP2C19-substrate:   0.407
CYP2C9-inhibitor:   0.667 CYP2C9-substrate:   0.096
CYP2D6-inhibitor:   0.899 CYP2D6-substrate:   0.686
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.989
CYP2B6-substrate:   0.011 CYP2C8-inhibitor:   0.994
HLM stability:   0.937
?
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):  10.356 Half-life (T1/2):  1.001

ADMET: Toxicity

hERG Blockers:  0.335 hERG Blockers (10um):  0.699
Human Hepatotoxicity (H-HT):  0.718 Drug-induced Liver Injury (DILI):  0.404
AMES Toxicity:  0.152 Rat Oral Acute Toxicity:  0.274
Maximum Recommended Daily Dose:  0.481 Skin Sensitization:  0.907
Carcinogencity:  0.313 Eye Corrosion:  0.144
Eye Irritation:  0.952 Respiratory Toxicity:  0.881
Drug-induced Neurotoxicity:  0.38 Ototoxicity:  0.418
Hematotoxicity:  0.274 Drug-induced Nephrotoxicity:  0.331
Genotoxicity:  0.063 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.136 Hek293 Cytotoxicity:  0.133
BCF:   2.294
?
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:   4.714
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.888
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.854
?
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
NPO1859 Lantana camara Species Verbenaceae Eukaryota aerial parts n.a. n.a. PMID[10869197]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. PMID[15974602]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[1812212]
NPO23546 Clausena lansium Species Rutaceae Eukaryota leaves n.a. n.a. PMID[19327990]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Stems n.a. n.a. PMID[22372931]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Roots n.a. n.a. PMID[24798144]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[26110519]
NPO23546 Clausena lansium Species Rutaceae Eukaryota Leaves n.a. n.a. PMID[26523463]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[29338260]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[30970599]
NPO51811 Myrcia eximia Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32059439]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32772473]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[33780581]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[36270431]
NPO58210 Anthemis palestina Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38005810]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[38257257]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[38893531]
NPO56519 Goniothalamus yunnanensis Genus Annonaceae Eukaryota n.a. n.a. n.a. PMID[39102300]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. PMID[39104562]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO1859 Lantana camara Species Verbenaceae Eukaryota leaves n.a. n.a. PMID[9834145]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10473 Spongia rimosa Species Spongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18039 Herba dendrobii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO28466 Torreya nucifera Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18039 Herba dendrobii n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23546 Clausena lansium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14041 Dendrobium findlayanum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1859 Lantana camara Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10473 Spongia rimosa Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13153 Callicarpa macrophylla Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28466 Torreya nucifera Species Taxaceae 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
NPO1859 Lantana camara Oil n.a. 0.6 n.a. n.a. % PMID[33780581]
NPO1859 Lantana camara Oil n.a. 0.2 n.a. n.a. % PMID[33780581]
NPO23546 Clausena lansium Oil n.a. 0.67 n.a. n.a. % PMID[30970599]
NPO23546 Clausena lansium Oil n.a. 1.05 n.a. n.a. % PMID[30970599]
NPO23546 Clausena lansium Oil n.a. 0.64 n.a. n.a. % PMID[30970599]
NPO51811 Myrcia eximia Oil n.a. 0.21 n.a. n.a. % PMID[32059439]
NPO56519 Goniothalamus yunnanensis Oil n.a. 0.2 n.a. n.a. % PMID[39102300]
NPO58210 Anthemis palestina Shade-dried n.a. 0.17 n.a. n.a. % PMID[38005810]
NPO9809 Scutellaria altissima Oil n.a. 0.47 n.a. n.a. % PMID[32772473]

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 NPC155129 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
0.6977 Remote Similarity NPC177331
0.6471 Remote Similarity NPC105249
0.6383 Remote Similarity NPC471521
0.6383 Remote Similarity NPC473356
0.6038 Remote Similarity NPC208906
0.5714 Remote Similarity NPC28054
0.5333 Remote Similarity NPC474407
0.5294 Remote Similarity NPC26157
0.5294 Remote Similarity NPC1811
0.5246 Remote Similarity NPC283284
0.5246 Remote Similarity NPC131801
0.5246 Remote Similarity NPC289911
0.5091 Remote Similarity NPC473355
0.5091 Remote Similarity NPC471573
0.5091 Remote Similarity NPC144745
0.5088 Remote Similarity NPC473379
0.5088 Remote Similarity NPC471549

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC155129 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