Natural Product: NPC45655

Natural Product IDNPC45655
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SHEOKDCVBGTHJG-QMMMGPOBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 71349601
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids

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 SHEOKDCVBGTHJG-QMMMGPOBSA-N
Standard InCHI InChI=1S/C15H16O2/c1-8-4-11-14(12(16)5-8)9(2)6-13-15(11)10(3)7-17-13/h6-8H,4-5H2,1-3H3/t8-/m0/s1
SMILES C[C@H]1Cc2c(c(C)cc3c2c(C)co3)C(=O)C1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   228.12 Volume:   246.725
?
Van der Waals volume.
Dense:   0.925 LogP:   3.564
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.392
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.833
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   0.0 Rigid Bonds:   16.0
TPSA:   30.21
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   3.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.686 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.289 Fsp3:   0.4
MCE-18:   55.857
?
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:   0.249 Fluc inhibitor:   0.335
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.715
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.217
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.561 Promiscuous compounds:   0.302

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.681 MDCK Permeability:   -4.588
Pgp-inhibitor:   0.956 Pgp-substrate:   0.135
PAMPA:   0.104
?
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):   0.001
20% Bioavailability (F20%):   0.013 30% Bioavailability (F30%):   0.07
50% Bioavailability (F50%):   0.543

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.31 MRP1:   0.991
Plasma Protein Binding (PPB):   92.951% Volume Distribution (VD):   0.333
Fu: 5.956%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.286
BSEP inhibitor:   0.999

ADMET: Metabolism

CYP1A2-inhibitor:   0.198 CYP1A2-substrate:   0.964
CYP2C19-inhibitor:   0.1 CYP2C19-substrate:   0.976
CYP2C9-inhibitor:   0.028 CYP2C9-substrate:   0.251
CYP2D6-inhibitor:   0.021 CYP2D6-substrate:   0.446
CYP3A4-inhibitor:   0.599 CYP3A4-substrate:   0.904
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.997
HLM stability:   0.994
?
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):  7.891 Half-life (T1/2):  0.276

ADMET: Toxicity

hERG Blockers:  0.088 hERG Blockers (10um):  0.431
Human Hepatotoxicity (H-HT):  0.769 Drug-induced Liver Injury (DILI):  0.923
AMES Toxicity:  0.779 Rat Oral Acute Toxicity:  0.718
Maximum Recommended Daily Dose:  0.86 Skin Sensitization:  0.923
Carcinogencity:  0.892 Eye Corrosion:  0.091
Eye Irritation:  0.986 Respiratory Toxicity:  0.881
Drug-induced Neurotoxicity:  0.793 Ototoxicity:  0.54
Hematotoxicity:  0.418 Drug-induced Nephrotoxicity:  0.71
Genotoxicity:  0.706 RPMI-8226 Immunitoxicity:  0.111
A549 Cytotoxicity:  0.251 Hek293 Cytotoxicity:  0.188
BCF:   2.381
?
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:   4.117
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.288
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.92
?
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
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota roots northern Saudi desert n.a. PMID[10924184]
NPO6831 Commiphora opobalsamum Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[18177010]
NPO8286 Porophyllum ruderale Species Asteraceae Eukaryota n.a. Along the Valencian coast, Spain 2020-Jun&Jul PMID[35161358]
NPO11719 Lamellomorpha strongylata Species Vulcanellidae Eukaryota n.a. n.a. n.a. PMID[9644054]
NPO6022 Cytisus supinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9036 Dipteryx lacunifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9883 Allium giganteum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10085 Aspergillus varians Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3693 Calpurnia aurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6831 Commiphora opobalsamum Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29336 Corynandra chelidonii Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4463 Cytisus canariensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24891 Elmerina caryae Species Aporpiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8286 Porophyllum ruderale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4964 Traversia baccharoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14610 Ophiopogon intermedius Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4236 Microscleroderma spirophora Species Scleritodermidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13613 Lophophora williamsii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11719 Lamellomorpha strongylata Species Vulcanellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5886 Fossombronia alaskana Species Fossombroniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25831 Siphonoglossa sessilis n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO5284 Ramalina hierrensis Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9639 Prunus puddum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8810 Pinus austriaca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2328 Lagochilus setulosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8297 Hydnellum caeruleum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1586 Gorgonocephalus chilensis Species Gorgonocephalidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8985 Gazania rigens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13613 Lophophora williamsii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8297 Hydnellum caeruleum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13613 Lophophora williamsii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4463 Cytisus canariensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25831 Siphonoglossa sessilis n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO2328 Lagochilus setulosus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9036 Dipteryx lacunifera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO817 Dictamnus angustifolius Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29336 Corynandra chelidonii Species Cleomaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8810 Pinus austriaca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1586 Gorgonocephalus chilensis Species Gorgonocephalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11719 Lamellomorpha strongylata Species Vulcanellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5284 Ramalina hierrensis Species Ramalinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24891 Elmerina caryae Species Aporpiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8985 Gazania rigens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7260 Angelica genuflexa Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9639 Prunus puddum Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4236 Microscleroderma spirophora Species Scleritodermidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13613 Lophophora williamsii Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4964 Traversia baccharoides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3693 Calpurnia aurea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9883 Allium giganteum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11707 Ruta chalepensis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14610 Ophiopogon intermedius Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8286 Porophyllum ruderale Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6831 Commiphora opobalsamum Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5886 Fossombronia alaskana Species Fossombroniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8297 Hydnellum caeruleum Species Thelephoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10085 Aspergillus varians Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6022 Cytisus supinus Species Fabaceae 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 NPC45655 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 NPC45655 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