Natural Product: NPC230298

Natural Product IDNPC230298
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZGIGZINMAOQWLX-HDVIWIBHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 1551480
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 ZGIGZINMAOQWLX-HDVIWIBHSA-N
Standard InCHI InChI=1S/C17H28O2/c1-14(2)8-6-9-15(3)10-7-11-16(4)12-13-19-17(5)18/h8,10,12H,6-7,9,11,13H2,1-5H3/b15-10+,16-12-
SMILES CC(=CCC/C(=C/CC/C(=CCOC(=O)C)/C)/C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   264.21 Volume:   309.623
?
Van der Waals volume.
Dense:   0.853 LogP:   5.659
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.68
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.064
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   4.0
TPSA:   26.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.457 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.742 Fsp3:   0.588
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:   0.248 Fluc inhibitor:   0.005
?
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:   0.015
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.993 Promiscuous compounds:   0.063

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.466 MDCK Permeability:   -4.738
Pgp-inhibitor:   0.997 Pgp-substrate:   0.019
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):   0.05
20% Bioavailability (F20%):   0.075 30% Bioavailability (F30%):   0.245
50% Bioavailability (F50%):   0.807

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.034 MRP1:   0.981
Plasma Protein Binding (PPB):   95.396% Volume Distribution (VD):   -0.317
Fu: 5.071%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.962 BCRP inhibitor:   0.021
BSEP inhibitor:   0.983

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.448
CYP2C19-inhibitor:   0.503 CYP2C19-substrate:   0.037
CYP2C9-inhibitor:   0.781 CYP2C9-substrate:   0.071
CYP2D6-inhibitor:   0.751 CYP2D6-substrate:   0.358
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.738
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.996
HLM stability:   0.991
?
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):  8.811 Half-life (T1/2):  0.749

ADMET: Toxicity

hERG Blockers:  0.054 hERG Blockers (10um):  0.432
Human Hepatotoxicity (H-HT):  0.498 Drug-induced Liver Injury (DILI):  0.039
AMES Toxicity:  0.186 Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.084 Skin Sensitization:  0.994
Carcinogencity:  0.29 Eye Corrosion:  0.794
Eye Irritation:  0.99 Respiratory Toxicity:  0.762
Drug-induced Neurotoxicity:  0.512 Ototoxicity:  0.225
Hematotoxicity:  0.329 Drug-induced Nephrotoxicity:  0.261
Genotoxicity:  0.011 RPMI-8226 Immunitoxicity:  0.033
A549 Cytotoxicity:  0.019 Hek293 Cytotoxicity:  0.028
BCF:   2.113
?
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:   4.921
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.321
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.969
?
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
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. fruit n.a. PMID[10606547]
NPO9348 Cananga odorata Species Annonaceae Eukaryota fruits n.a. n.a. PMID[11374955]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota rhizomes n.a. n.a. PMID[12951092]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. rhizome n.a. PMID[15930771]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. leaf n.a. PMID[17999353]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota Roots; Tubers n.a. n.a. PMID[19639966]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[21504145]
NPO9348 Cananga odorata Species Annonaceae Eukaryota flower buds Thailand n.a. PMID[24601675]
NPO54898 Artemisia magellanica Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[31241852]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[34771092]
NPO44665 Achillea coarctata Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36006860]
NPO57639 Cuscuta campestris Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[37183783]
NPO56766 Centranthus ruber Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[37934763]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[38786901]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[38999684]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[39459015]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO44665 Achillea coarctata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13346 Lindera strichnifolia Species Tineidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13346 Lindera strichnifolia Species Tineidae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25443 Citrus reticulata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10082 Citrus unshiu Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9348 Cananga odorata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5033 Alpinia galanga Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4682 Lindera aggregata Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25443 Citrus reticulata Species Rutaceae 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
NPO44665 Achillea coarctata Oil n.a. 0.1 n.a. n.a. % PMID[36006860]
NPO44665 Achillea coarctata Oil n.a. 0.3 n.a. n.a. % PMID[36006860]
NPO54898 Artemisia magellanica Oil n.a. 0.4 n.a. n.a. % PMID[31241852]
NPO56766 Centranthus ruber Oil Aerial parts 3.15 n.a. n.a. % PMID[37934763]
NPO56766 Centranthus ruber Oil Roots 7.68 n.a. n.a. % PMID[37934763]
NPO57639 Cuscuta campestris Oil Stems 0.51±0.02 n.a. n.a. % PMID[37183783]
NPO9348 Cananga odorata Oil n.a. 2.90 n.a. n.a. % PMID[39459015]
NPO9348 Cananga odorata Oil n.a. 3.15 n.a. n.a. % PMID[39459015]

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 NPC230298 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 NPC197467
0.9286 High Similarity NPC47946
0.9286 High Similarity NPC26600
0.7273 Intermediate Similarity NPC135698
0.7059 Intermediate Similarity NPC236338
0.5758 Remote Similarity NPC128280
0.575 Remote Similarity NPC221379
0.575 Remote Similarity NPC318549
0.575 Remote Similarity NPC600969
0.5556 Remote Similarity NPC82465
0.5526 Remote Similarity NPC610812
0.5455 Remote Similarity NPC271641
0.5319 Remote Similarity NPC294938
0.525 Remote Similarity NPC314590
0.5217 Remote Similarity NPC249850
0.5208 Remote Similarity NPC223679
0.5208 Remote Similarity NPC254095
0.52 Remote Similarity NPC482045
0.5172 Remote Similarity NPC123965
0.5172 Remote Similarity NPC115959
0.5152 Remote Similarity NPC270706
0.5152 Remote Similarity NPC185839
0.5152 Remote Similarity NPC180840
0.5128 Remote Similarity NPC96663
0.5106 Remote Similarity NPC21946
0.5102 Remote Similarity NPC101622

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC230298 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
0.7879 Intermediate Similarity NPD6927 Phase 3
0.5476 Remote Similarity NPD2268 Discontinued
0.5152 Remote Similarity NPD5783 Phase 3

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