Structure

Physi-Chem Properties

Molecular Weight:  350.21
Volume:  358.929
LogP:  0.309
LogD:  0.229
LogS:  -3.405
# Rotatable Bonds:  1
TPSA:  97.99
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  4
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.53
Synthetic Accessibility Score:  6.192
Fsp3:  0.85
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.062
MDCK Permeability:  4.9515888349560555e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.082
Human Intestinal Absorption (HIA):  0.016
20% Bioavailability (F20%):  0.275
30% Bioavailability (F30%):  0.661

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.36
Plasma Protein Binding (PPB):  31.435352325439453%
Volume Distribution (VD):  0.606
Pgp-substrate:  64.67205810546875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.273
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.662
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.06
CYP2D6-inhibitor:  0.002
CYP2D6-substrate:  0.101
CYP3A4-inhibitor:  0.038
CYP3A4-substrate:  0.201

ADMET: Excretion

Clearance (CL):  3.286
Half-life (T1/2):  0.623

ADMET: Toxicity

hERG Blockers:  0.176
Human Hepatotoxicity (H-HT):  0.123
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.229
Rat Oral Acute Toxicity:  0.957
Maximum Recommended Daily Dose:  0.974
Skin Sensitization:  0.651
Carcinogencity:  0.036
Eye Corrosion:  0.005
Eye Irritation:  0.045
Respiratory Toxicity:  0.978

Download Data

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General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC15362

Natural Product ID:  NPC15362
Common Name*:   NQABJFRJEKCYEC-GFPDKIFBSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  NQABJFRJEKCYEC-GFPDKIFBSA-N
Standard InCHI:  InChI=1S/C20H30O5/c1-10-11-4-5-12-19(3)13(18(2,9-21)7-6-14(19)22)8-15(23)20(12,16(10)24)17(11)25/h11-15,17,21-23,25H,1,4-9H2,2-3H3/t11-,12-,13+,14-,15+,17+,18+,19-,20-/m0/s1
SMILES:  C=C1[C@@H]2CC[C@H]3[C@@]4(C)[C@H](C[C@H]([C@@]3(C1=O)[C@@H]2O)O)[C@](C)(CC[C@@H]4O)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10066480
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003782] Kaurane diterpenoids

*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
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)94333-4]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[16792416]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. PMID[17190457]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota Heartwood India n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. heartwood n.a. PMID[21488654]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota heartwood n.a. n.a. PMID[21784631]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18360 Isodon weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1238 Gentiana brachyphylla Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8694 Picrasma crenata Species Simaroubaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5400 Lycoris aurea Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18360 Isodon weisiensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7594 Muricea californica Species Plexauridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6120 Attalea funifera Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3038 Veronica linariifolia Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3902 Aglaia edulis Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11368 Leontodon tuberosus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8191 Lecanora epanora Species Lecanoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5138 Colebrookea oppositifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4558 Polysaccum crassipes n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO1087 Pterocarpus santalinus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO265 Helminthosporium zizaniae Species Massarinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1531 Chlorella sorokiniana Species Chlorellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4800 Cyrtocymura cincta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15395 Euphorbia portlandica Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21411 Santolina magonica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO688 Scorzonera cretica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1238 Gentiana brachyphylla Species Gentianaceae 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

☑ 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 NPC15362 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 NPC15362 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