Natural Product: NPC269499

Natural Product IDNPC269499
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JIGCTXHIECXYRJ-LTGZKZEYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6428538
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0001357] Acyclic diterpenoids

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 JIGCTXHIECXYRJ-LTGZKZEYSA-N
Standard InCHI InChI=1S/C22H42O2/c1-18(2)10-7-11-19(3)12-8-13-20(4)14-9-15-21(5)16-17-24-22(6)23/h16,18-20H,7-15,17H2,1-6H3/b21-16+
SMILES CC(C)CCCC(C)CCCC(C)CCC/C(=C/COC(=O)C)/C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   338.32 Volume:   401.376
?
Van der Waals volume.
Dense:   0.843 LogP:   7.69
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.346
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -7.122
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   2.0
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:   0.253 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.298 Fsp3:   0.864
MCE-18:   5.0
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.389 Fluc inhibitor:   0.318
?
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:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.987 Promiscuous compounds:   0.013

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.99 MDCK Permeability:   -4.802
Pgp-inhibitor:   0.003 Pgp-substrate:   0.004
PAMPA:   0.007
?
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%):   0.005 30% Bioavailability (F30%):   0.705
50% Bioavailability (F50%):   0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.803 MRP1:   0.926
Plasma Protein Binding (PPB):   95.631% Volume Distribution (VD):   0.042
Fu: 4.484%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.446
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.502
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.976
CYP2C19-inhibitor:   0.853 CYP2C19-substrate:   0.993
CYP2C9-inhibitor:   0.908 CYP2C9-substrate:   0.615
CYP2D6-inhibitor:   0.012 CYP2D6-substrate:   0.011
CYP3A4-inhibitor:   0.022 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.01 CYP2C8-inhibitor:   1.0
HLM stability:   0.976
?
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):  6.389 Half-life (T1/2):  0.266

ADMET: Toxicity

hERG Blockers:  0.182 hERG Blockers (10um):  0.673
Human Hepatotoxicity (H-HT):  0.571 Drug-induced Liver Injury (DILI):  0.027
AMES Toxicity:  0.302 Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.223 Skin Sensitization:  0.994
Carcinogencity:  0.507 Eye Corrosion:  0.897
Eye Irritation:  0.984 Respiratory Toxicity:  0.641
Drug-induced Neurotoxicity:  0.083 Ototoxicity:  0.398
Hematotoxicity:  0.431 Drug-induced Nephrotoxicity:  0.176
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.101
A549 Cytotoxicity:  0.084 Hek293 Cytotoxicity:  0.032
BCF:   2.193
?
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:   5.19
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.283
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.499
?
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
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0040-4020(01)83306-8]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. DOI[10.1021/np50031a011]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. seed n.a. PMID[17345316]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18303850]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18681481]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19344127]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. aerial part n.a. PMID[21902175]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Whole Plant Dongshan, Nanjing, Jiangsu Province, China 2012-NOV PMID[25314138]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[26000707]
NPO52048 Inula viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[30874370]
NPO47856 Ansellia africana Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[31140321]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[32880179]
NPO47856 Ansellia africana Species Orchidaceae Eukaryota n.a. n.a. n.a. PMID[34361724]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37446590]
NPO64536 Barleria albostellata Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[37446958]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[37447270]
NPO52461 Calyptocarpus vialis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[37450214]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[38192648]
NPO52048 Inula viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[38245842]
NPO63069 Cinnamomum burmanni Species Lauraceae Eukaryota n.a. n.a. n.a. PMID[38542843]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[38927152]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[39064881]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[39621736]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. PMID[39769283]
NPO1942 Piper philippinum Species Piperaceae Eukaryota n.a. n.a. n.a. PMID[39771253]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO52048 Inula viscosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1942 Piper philippinum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. Database[FooDB]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO681 Mesua ferrea Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20837 Ipomoea aquatica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28260 Senna alexandrina Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7513 Cannabis sativa Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13272 Ulva lactuca Species Ulvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1942 Piper philippinum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO681 Mesua ferrea Species Calophyllaceae 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
NPO13272 Ulva lactuca n.a. n.a. 3.88 n.a. n.a. % PMID[39769283]
NPO1942 Piper philippinum Oil Aerial parts 0.164 ± 0.010 n.a. n.a. % PMID[39771253]
NPO20837 Ipomoea aquatica n.a. n.a. 0.22 n.a. n.a. % PMID[38192648]
NPO47856 Ansellia africana n.a. n.a. 1.16 n.a. n.a. % PMID[34361724]
NPO52048 Inula viscosa Oil n.a. 0.6 n.a. n.a. % PMID[30874370]
NPO52048 Inula viscosa Oil n.a. 0.8 n.a. n.a. % PMID[30874370]
NPO52048 Inula viscosa Oil n.a. 0.7 n.a. n.a. % PMID[30874370]
NPO52048 Inula viscosa Oil n.a. 0.4 n.a. n.a. % PMID[30874370]
NPO52048 Inula viscosa Oil n.a. 0.2 n.a. n.a. % PMID[30874370]
NPO52461 Calyptocarpus vialis n.a. n.a. 3.05 n.a. n.a. % PMID[37450214]
NPO63069 Cinnamomum burmanni Oil n.a. 4.66 n.a. n.a. % PMID[38542843]
NPO63069 Cinnamomum burmanni Oil n.a. 6.77 n.a. n.a. % PMID[38542843]
NPO63069 Cinnamomum burmanni Oil n.a. 4.26 n.a. n.a. % PMID[38542843]
NPO64536 Barleria albostellata n.a. Leaves 7.29 n.a. n.a. % PMID[37446958]
NPO681 Mesua ferrea Ethanolic extract Leaves 0.32 n.a. n.a. % PMID[39621736]
NPO7513 Cannabis sativa Oil Roots 0.21 ± 0.21 n.a. n.a. % PMID[37446590]
NPO7513 Cannabis sativa Oil Roots 8.35 ± 1.01 n.a. n.a. % PMID[37446590]
NPO7513 Cannabis sativa Oil Roots 0.09 ± 0.05 n.a. n.a. % PMID[37446590]

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 NPC269499 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 NPC96663
0.6512 Remote Similarity NPC329698
0.6444 Remote Similarity NPC34883
0.6304 Remote Similarity NPC472264
0.5405 Remote Similarity NPC47946
0.5405 Remote Similarity NPC26600
0.5128 Remote Similarity NPC197467

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC269499 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