Structure

Physi-Chem Properties

Molecular Weight:  210.23
Volume:  259.44
LogP:  6.311
LogD:  6.006
LogS:  -5.597
# Rotatable Bonds:  4
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.603
Synthetic Accessibility Score:  3.655
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.489
MDCK Permeability:  1.682983747741673e-05
Pgp-inhibitor:  0.401
Pgp-substrate:  0.161
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.933

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.412
Plasma Protein Binding (PPB):  96.61078643798828%
Volume Distribution (VD):  2.599
Pgp-substrate:  2.8880672454833984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.653
CYP1A2-substrate:  0.604
CYP2C19-inhibitor:  0.444
CYP2C19-substrate:  0.879
CYP2C9-inhibitor:  0.758
CYP2C9-substrate:  0.43
CYP2D6-inhibitor:  0.061
CYP2D6-substrate:  0.066
CYP3A4-inhibitor:  0.289
CYP3A4-substrate:  0.396

ADMET: Excretion

Clearance (CL):  10.288
Half-life (T1/2):  0.131

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.054
Drug-inuced Liver Injury (DILI):  0.883
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.033
Skin Sensitization:  0.948
Carcinogencity:  0.384
Eye Corrosion:  0.988
Eye Irritation:  0.967
Respiratory Toxicity:  0.146

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

  Natural Product: NPC109685

Natural Product ID:  NPC109685
Common Name*:   XWSLVXPTZNNNQD-XGUBFFRZSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  XWSLVXPTZNNNQD-XGUBFFRZSA-N
Standard InCHI:  InChI=1S/C15H30/c1-6-12(4)9-14-10-13(5)7-8-15(14)11(2)3/h11-15H,6-10H2,1-5H3/t12-,13+,14-,15-/m0/s1
SMILES:  CC[C@H](C)C[C@H]1C[C@H](C)CC[C@H]1C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] 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
NPO24313 Calyptranthes pallens Species Myrtaceae Eukaryota leaves and twigs Southern Florida n.a. PMID[15844953]
NPO28043 Streblus asper Species Moraceae Eukaryota Roots n.a. n.a. PMID[23434030]
NPO28043 Streblus asper Species Moraceae Eukaryota n.a. n.a. n.a. PMID[4093781]
NPO22205 Trixis vauthieri Species n.a. n.a. n.a. n.a. n.a. PMID[9287419]
NPO24069 Swertia patens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO24348 Erythroxylum novogranatense Species Erythroxylaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24069 Swertia patens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24069 Swertia patens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22620 Baliospermum montanum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24348 Erythroxylum novogranatense Species Erythroxylaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23573 Humbertia madagascariensis Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23985 Mollisia caesia Species Dermateaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22620 Baliospermum montanum Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24032 Streptomyces omiyaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23070 Corallina pilulifera Species Corallinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20492 Streptomyces subrutilus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO3972 Clinopodium vulgare Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8743 Pectobacterium carotovorum Species Pectobacteriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22205 Trixis vauthieri Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO28043 Streblus asper Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14505 Lactobacillus reuteri Species Lactobacillaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22897 Streptomyces limosus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24348 Erythroxylum novogranatense Species Erythroxylaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23755 Betula humilis Species Betulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24069 Swertia patens Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24313 Calyptranthes pallens Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23940 Thalictrum urbaini Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23619 Mycale adhaerens Species Mycalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23385 Sarcophyton mililatensis Species Alcyoniidae 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 NPC109685 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 NPC109685 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