Structure

Physi-Chem Properties

Molecular Weight:  204.19
Volume:  239.69
LogP:  4.054
LogD:  3.413
LogS:  -5.072
# Rotatable Bonds:  0
TPSA:  0.0
# H-Bond Aceptor:  0
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  0

MedChem Properties

QED Drug-Likeness Score:  0.507
Synthetic Accessibility Score:  5.17
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:  -4.637
MDCK Permeability:  1.4622171875089407e-05
Pgp-inhibitor:  0.013
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.896
30% Bioavailability (F30%):  0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.262
Plasma Protein Binding (PPB):  96.32391357421875%
Volume Distribution (VD):  1.622
Pgp-substrate:  3.8729236125946045%

ADMET: Metabolism

CYP1A2-inhibitor:  0.496
CYP1A2-substrate:  0.835
CYP2C19-inhibitor:  0.708
CYP2C19-substrate:  0.935
CYP2C9-inhibitor:  0.312
CYP2C9-substrate:  0.482
CYP2D6-inhibitor:  0.068
CYP2D6-substrate:  0.404
CYP3A4-inhibitor:  0.695
CYP3A4-substrate:  0.613

ADMET: Excretion

Clearance (CL):  7.737
Half-life (T1/2):  0.171

ADMET: Toxicity

hERG Blockers:  0.074
Human Hepatotoxicity (H-HT):  0.29
Drug-inuced Liver Injury (DILI):  0.178
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.056
Maximum Recommended Daily Dose:  0.049
Skin Sensitization:  0.797
Carcinogencity:  0.503
Eye Corrosion:  0.959
Eye Irritation:  0.962
Respiratory Toxicity:  0.85

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

  Natural Product: NPC129872

Natural Product ID:  NPC129872
Common Name*:   SAOJPWFHRMUCFN-MYPMTAMASA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SAOJPWFHRMUCFN-MYPMTAMASA-N
Standard InCHI:  InChI=1S/C15H24/c1-11-6-9-14(4)12(2)10-13(3)7-5-8-15(11,13)14/h10-11H,5-9H2,1-4H3/t11-,13+,14+,15-/m0/s1
SMILES:  C[C@H]1CC[C@]2(C)C(=C[C@@]3(C)CCC[C@@]123)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11030948
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002004] Triquinane sesquiterpenoids
            • [CHEMONTID:0003582] Angular triquinanes

*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
NPO6601 Canscora decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0031-9422(00)89890-8]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. PMID[22700234]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. leaf n.a. PMID[24354205]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. twig n.a. PMID[24354205]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[29303577]
NPO6601 Canscora decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[807707]
NPO18328 Leontopodium alpinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4992 Goniothalamus griffithii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4992 Goniothalamus griffithii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18328 Leontopodium alpinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4992 Goniothalamus griffithii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17357 Bactrocera kraussi Species Tephritidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18266 Microsphaeropsis olivacea Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4992 Goniothalamus griffithii Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18678 Actinomadura pelletieri Species Thermomonosporaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO18931 Buellia canescens Species Caliciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19795 Xanthoparmelia loxodes Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18328 Leontopodium alpinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17904 Cassia renigera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1171 Gilibertia trifida n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10119 Aptosimum spinescens Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17639 Stevia achalensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6601 Canscora decussata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19048 Pinellia ternata Species Araceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12182 Murraya exotica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO438 Butia capitata Species Arecaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1672 Apostichopus japonicus Species Stichopodidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18770 Euphausia pacifica Species Euphausiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19071 Alliaria petiolata Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7680 Hopea hainanensis Species Dipterocarpaceae 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 NPC129872 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 NPC129872 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