Structure

Physi-Chem Properties

Molecular Weight:  222.2
Volume:  257.037
LogP:  4.077
LogD:  3.741
LogS:  -3.688
# Rotatable Bonds:  1
TPSA:  20.23
# H-Bond Aceptor:  1
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.667
Synthetic Accessibility Score:  4.095
Fsp3:  0.867
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.618
MDCK Permeability:  2.2519863705383614e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.024
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.143
Plasma Protein Binding (PPB):  84.7520980834961%
Volume Distribution (VD):  1.271
Pgp-substrate:  17.56572151184082%

ADMET: Metabolism

CYP1A2-inhibitor:  0.049
CYP1A2-substrate:  0.53
CYP2C19-inhibitor:  0.128
CYP2C19-substrate:  0.907
CYP2C9-inhibitor:  0.124
CYP2C9-substrate:  0.329
CYP2D6-inhibitor:  0.024
CYP2D6-substrate:  0.493
CYP3A4-inhibitor:  0.275
CYP3A4-substrate:  0.332

ADMET: Excretion

Clearance (CL):  7.446
Half-life (T1/2):  0.271

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.054
Drug-inuced Liver Injury (DILI):  0.033
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.187
Skin Sensitization:  0.426
Carcinogencity:  0.081
Eye Corrosion:  0.983
Eye Irritation:  0.981
Respiratory Toxicity:  0.362

Download Data

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

  Natural Product: NPC259138

Natural Product ID:  NPC259138
Common Name*:   DPQYOKVMVCQHMY-TUVASFSCSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DPQYOKVMVCQHMY-TUVASFSCSA-N
Standard InCHI:  InChI=1S/C15H26O/c1-11(2)12-6-9-14(3)7-5-8-15(4,16)13(14)10-12/h12-13,16H,1,5-10H2,2-4H3/t12-,13-,14-,15+/m1/s1
SMILES:  C=C(C)[C@@H]1CC[C@@]2(C)CCC[C@@](C)([C@@H]2C1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11877394
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids

*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
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. Database[FooDB]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO22666 Haematococcus lacustris Species Haematococcaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13274 Illicium verum Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7998 Senecio paludaffinis Species Asteraceae 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 NPC259138 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 NPC259138 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