Natural Product: NPC181051

Natural Product IDNPC181051
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZLJPQFLGGAYZAN-UMVBOHGHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 10585158
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000129] Alcohols and polyols
          • [CHEMONTID:0001661] Secondary alcohols

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 ZLJPQFLGGAYZAN-UMVBOHGHSA-N
Standard InCHI InChI=1S/C15H26O/c1-11-6-7-13(16)15(4)9-5-8-14(2,3)12(15)10-11/h10,12-13,16H,5-9H2,1-4H3/t12-,13-,15-/m1/s1
SMILES CC1=C[C@@H]2C(C)(C)CCC[C@@]2(C)[C@@H](CC1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   222.2 Volume:   257.037
?
Van der Waals volume.
Dense:   0.864 LogP:   3.117
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.102
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.973
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   12.0
TPSA:   20.23
?
Topological Polar Surface Area.
 H-Bond Acceptor:   1.0
H-Bond Donor:   1.0 Rings:   2.0
Heavy Atoms:   1.0

MedChem Properties

QED Drug-Likeness Score:   0.616 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.929 Fsp3:   0.867
MCE-18:   39.643
?
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:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.333 Fluc inhibitor:   0.008
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.014
?
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:   0.883 Promiscuous compounds:   0.226

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.687 MDCK Permeability:   -4.741
Pgp-inhibitor:   0.878 Pgp-substrate:   0.107
PAMPA:   0.811
?
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):   0.18
20% Bioavailability (F20%):   0.765 30% Bioavailability (F30%):   0.537
50% Bioavailability (F50%):   0.972

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.343 MRP1:   0.459
Plasma Protein Binding (PPB):   94.29% Volume Distribution (VD):   -0.075
Fu: 5.269%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.919 BCRP inhibitor:   0.385
BSEP inhibitor:   0.933

ADMET: Metabolism

CYP1A2-inhibitor:   0.699 CYP1A2-substrate:   0.155
CYP2C19-inhibitor:   0.997 CYP2C19-substrate:   0.028
CYP2C9-inhibitor:   0.329 CYP2C9-substrate:   0.03
CYP2D6-inhibitor:   0.839 CYP2D6-substrate:   0.006
CYP3A4-inhibitor:   0.219 CYP3A4-substrate:   0.038
CYP2B6-substrate:   0.711 CYP2C8-inhibitor:   0.003
HLM stability:   0.602
?
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):  12.546 Half-life (T1/2):  1.421

ADMET: Toxicity

hERG Blockers:  0.04 hERG Blockers (10um):  0.27
Human Hepatotoxicity (H-HT):  0.661 Drug-induced Liver Injury (DILI):  0.328
AMES Toxicity:  0.558 Rat Oral Acute Toxicity:  0.368
Maximum Recommended Daily Dose:  0.404 Skin Sensitization:  0.936
Carcinogencity:  0.788 Eye Corrosion:  0.765
Eye Irritation:  0.978 Respiratory Toxicity:  0.765
Drug-induced Neurotoxicity:  0.213 Ototoxicity:  0.301
Hematotoxicity:  0.432 Drug-induced Nephrotoxicity:  0.519
Genotoxicity:  0.074 RPMI-8226 Immunitoxicity:  0.058
A549 Cytotoxicity:  0.26 Hek293 Cytotoxicity:  0.184
BCF:   2.182
?
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:   3.641
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.676
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.326
?
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
NPO7657 Plectranthus ornatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[12398532]
NPO20112 Syncephalastrum racemosum Species Syncephalastraceae Eukaryota n.a. n.a. n.a. PMID[18558746]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. fruit n.a. PMID[21619045]
NPO13906 Ficus mucuso Species Moraceae Eukaryota figs Tongolo-Yaound, in the Central Region of Cameroon 2008-JUN PMID[21619045]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[23387901]
NPO51811 Myrcia eximia Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32059439]
NPO52078 Siparuna muricata Species Siparunaceae Eukaryota n.a. n.a. n.a. PMID[34063513]
NPO48225 Hyptis crenata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[36113677]
NPO52078 Siparuna muricata Species Siparunaceae Eukaryota n.a. n.a. n.a. PMID[36671283]
NPO20154 Cedrus atlantica Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[37049738]
NPO48225 Hyptis crenata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37110606]
NPO7657 Plectranthus ornatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37226591]
NPO7657 Plectranthus ornatus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37764258]
NPO17503 Conospermum incurvum Species n.a. n.a. n.a. n.a. n.a. PMID[7853001]
NPO16895 Croton sarcopetalus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20469 Acer caesium Species Aceraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19608 Aconitum likiangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21612 Anthelia glauca Species Xeniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21419 Biscogniauxia mediterranea Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19749 Carpolobia glabrescens Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3030 Chaenorhinum villosum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17503 Conospermum incurvum Species n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO19874 Polygonatum glaberrimum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21134 Thaumetopoea pityocampa Species Notodontidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1550 Talaromyces purpureogenus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20112 Syncephalastrum racemosum Species Syncephalastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13003 Sogatella furcifera Species Delphacidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20044 Schistostephium crataegifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21224 Rubus pinfaensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7765 Quercus spicata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18782.1 Pulsatilla cernua var. koreana Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20154 Cedrus atlantica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18806 Neodilsea yendoana Species Dumontiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21540 Naucleopsis stipularis Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21673 Lupinus caudatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17763 Lobularia elongata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12730 Heracleum maximum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20925 Fusarium culmorum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20662 Epinephelus drummondhayi Species Serranidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21000 Elysia halimedae Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12730 Heracleum maximum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20154 Cedrus atlantica Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18782.1 Pulsatilla cernua var. koreana Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18782.1 Pulsatilla cernua var. koreana Varieties Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3030 Chaenorhinum villosum Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19749 Carpolobia glabrescens Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13003 Sogatella furcifera Species Delphacidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21540 Naucleopsis stipularis Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20112 Syncephalastrum racemosum Species Syncephalastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7765 Quercus spicata Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1550 Talaromyces purpureogenus Species Trichocomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13906 Ficus mucuso Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21000 Elysia halimedae Species Placobranchidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20925 Fusarium culmorum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16895 Croton sarcopetalus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21224 Rubus pinfaensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18806 Neodilsea yendoana Species Dumontiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21134 Thaumetopoea pityocampa Species Notodontidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17503 Conospermum incurvum Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO20469 Acer caesium Species Aceraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7591 Cedrus deodara Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12730 Heracleum maximum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20044 Schistostephium crataegifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19608 Aconitum likiangense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19874 Polygonatum glaberrimum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21419 Biscogniauxia mediterranea Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21612 Anthelia glauca Species Xeniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17763 Lobularia elongata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20662 Epinephelus drummondhayi Species Serranidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21673 Lupinus caudatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7657 Plectranthus ornatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20154 Cedrus atlantica Species Pinaceae 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
NPO48225 Hyptis crenata Oil n.a. 0.1 n.a. n.a. % PMID[37110606]
NPO51811 Myrcia eximia Oil n.a. 3.49 n.a. n.a. % PMID[32059439]
NPO52078 Siparuna muricata n.a. Leaves 0.19 n.a. n.a. % PMID[36671283]
NPO7657 Plectranthus ornatus Oil n.a. 0.21 n.a. n.a. % PMID[37764258]

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 NPC181051 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
NPC

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC181051 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