Structure

Physi-Chem Properties

Molecular Weight:  326.32
Volume:  386.716
LogP:  8.871
LogD:  4.46
LogS:  -7.042
# Rotatable Bonds:  19
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.196
Synthetic Accessibility Score:  1.755
Fsp3:  0.952
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.964
MDCK Permeability:  1.1240201274631545e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.955
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.109
Plasma Protein Binding (PPB):  97.16625213623047%
Volume Distribution (VD):  3.112
Pgp-substrate:  1.3105305433273315%

ADMET: Metabolism

CYP1A2-inhibitor:  0.173
CYP1A2-substrate:  0.183
CYP2C19-inhibitor:  0.299
CYP2C19-substrate:  0.063
CYP2C9-inhibitor:  0.103
CYP2C9-substrate:  0.955
CYP2D6-inhibitor:  0.268
CYP2D6-substrate:  0.041
CYP3A4-inhibitor:  0.29
CYP3A4-substrate:  0.04

ADMET: Excretion

Clearance (CL):  4.655
Half-life (T1/2):  0.143

ADMET: Toxicity

hERG Blockers:  0.366
Human Hepatotoxicity (H-HT):  0.023
Drug-inuced Liver Injury (DILI):  0.426
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.016
Skin Sensitization:  0.964
Carcinogencity:  0.042
Eye Corrosion:  0.948
Eye Irritation:  0.949
Respiratory Toxicity:  0.893

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  Natural Product: NPC13483

Natural Product ID:  NPC13483
Common Name*:   QGBRLVONZXHAKJ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QGBRLVONZXHAKJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C21H42O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21(22)23-2/h3-20H2,1-2H3
SMILES:  CCCCCCCCCCCCCCCCCCCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   14259
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters
          • [CHEMONTID:0003417] Fatty acid methyl esters

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1002/elan.200403102]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2012.02.124]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[11077184]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. seed n.a. PMID[11540412]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. leaf n.a. PMID[15894448]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. root n.a. PMID[15894448]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota aerial parts purchased in Juhuacun herbal market, Kunming, Yunnan Province, China 2002-Oct PMID[16562826]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flowers n.a. n.a. PMID[17328234]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[17548953]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[18321056]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[18357994]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. root n.a. PMID[20707067]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. rhizome n.a. PMID[20707067]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. leaf n.a. PMID[21598983]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower n.a. PMID[21804227]
NPO29279 Aralia elata Species Araliaceae Eukaryota bark n.a. n.a. PMID[21889336]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. flower bud n.a. PMID[21942812]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota flower buds Henan province, China 2005-MAY PMID[21942812]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. leaf n.a. PMID[22026410]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. leaf n.a. PMID[23265495]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota Flower buds n.a. n.a. PMID[24279769]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. PMID[24675423]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Bako, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Enemore, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Gedo, Ethiopia PMID[24926420]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. Holleta, Ethiopia PMID[24926420]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25333853]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. PMID[8377022]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21824 Lycopus lucidus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO201 Gmelina arborea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO28211 Valeriana jatamansii Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29279 Aralia elata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29279 Aralia elata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO201 Gmelina arborea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28211 Valeriana jatamansii Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21824 Lycopus lucidus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29279 Aralia elata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30526 0topterygium incisum n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28211 Valeriana jatamansii Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21824 Lycopus lucidus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31286 Dolichos lablab Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO201 Gmelina arborea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21824 Lycopus lucidus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO27018 Cynomorium songaricum Species Cynomoriaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12006 Apis mellifera Species Apidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11045 Paederia scandens Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1515 Lonicera japonica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18873.1 Salmonella enterica subsp. enterica serovar anatum Subspecies Enterobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO29279 Aralia elata Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3052 Shorea resina-nigra Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10952 Camelina sativa Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24778 Sesamum orientale Species Pedaliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7893 Xanthoparmelia camtschadalis Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2790 Anthopleura elegantissima Species Actiniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21824 Lycopus lucidus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11238 Ocotea suaveolens Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18275 Struthiopteris amabilis Species Blechnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3578 Andrographis paniculata Species Acanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO201 Gmelina arborea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae 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 NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO12006 NPC13483 n.a. n.a. 0.004 n.a. n.a. % PMID[24926420]
NPO12006 NPC13483 n.a. n.a. 0.01 n.a. n.a. % PMID[24926420]
NPO12006 NPC13483 n.a. n.a. 0.007 n.a. n.a. % PMID[24926420]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC13483 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC13483 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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