Structure

Physi-Chem Properties

Molecular Weight:  122.11
Volume:  144.471
LogP:  3.639
LogD:  3.052
LogS:  -3.536
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.433
Synthetic Accessibility Score:  4.313
Fsp3:  0.778
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.462
MDCK Permeability:  1.846724990173243e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.872
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.124
30% Bioavailability (F30%):  0.259

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.535
Plasma Protein Binding (PPB):  94.44866943359375%
Volume Distribution (VD):  3.895
Pgp-substrate:  3.297032117843628%

ADMET: Metabolism

CYP1A2-inhibitor:  0.676
CYP1A2-substrate:  0.909
CYP2C19-inhibitor:  0.334
CYP2C19-substrate:  0.841
CYP2C9-inhibitor:  0.15
CYP2C9-substrate:  0.679
CYP2D6-inhibitor:  0.033
CYP2D6-substrate:  0.873
CYP3A4-inhibitor:  0.139
CYP3A4-substrate:  0.345

ADMET: Excretion

Clearance (CL):  13.905
Half-life (T1/2):  0.384

ADMET: Toxicity

hERG Blockers:  0.056
Human Hepatotoxicity (H-HT):  0.4
Drug-inuced Liver Injury (DILI):  0.337
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.03
Maximum Recommended Daily Dose:  0.26
Skin Sensitization:  0.827
Carcinogencity:  0.27
Eye Corrosion:  0.986
Eye Irritation:  0.989
Respiratory Toxicity:  0.633

Download Data

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

  Natural Product: NPC108432

Natural Product ID:  NPC108432
Common Name*:   LSIXBBPOJBJQHN-DTORHVGOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LSIXBBPOJBJQHN-DTORHVGOSA-N
Standard InCHI:  InChI=1S/C9H14/c1-6-7(2)9-4-3-8(6)5-9/h8-9H,3-5H2,1-2H3/t8-,9+
SMILES:  CC1=C(C)[C@@H]2CC[C@H]1C2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11457687
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004475] Unsaturated hydrocarbons
        • [CHEMONTID:0004622] Branched unsaturated hydrocarbons

*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
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. PMID[15974602]
NPO31577.1 Michelia compressa var. formosana Varieties Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30555 Mentha rotundifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17234.1 Michelia compressa var. formosana Varieties Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21286 Lignum pterocarpi indici n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30555 Mentha rotundifolia Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31577.1 Michelia compressa var. formosana Varieties Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17691 Santalum album Species Santalaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10561 Mentha suaveolens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17691 Santalum album Species Santalaceae 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 NPC108432 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 NPC108432 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