Structure

Physi-Chem Properties

Molecular Weight:  248.14
Volume:  260.788
LogP:  4.003
LogD:  3.084
LogS:  -3.703
# Rotatable Bonds:  0
TPSA:  45.9
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.566
Synthetic Accessibility Score:  4.819
Fsp3:  0.6
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:  -4.659
MDCK Permeability:  2.140839205821976e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.319
30% Bioavailability (F30%):  0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.222
Plasma Protein Binding (PPB):  95.23213195800781%
Volume Distribution (VD):  2.328
Pgp-substrate:  5.048487186431885%

ADMET: Metabolism

CYP1A2-inhibitor:  0.103
CYP1A2-substrate:  0.453
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.698
CYP2C9-inhibitor:  0.09
CYP2C9-substrate:  0.412
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.506
CYP3A4-inhibitor:  0.069
CYP3A4-substrate:  0.198

ADMET: Excretion

Clearance (CL):  12.463
Half-life (T1/2):  0.495

ADMET: Toxicity

hERG Blockers:  0.003
Human Hepatotoxicity (H-HT):  0.811
Drug-inuced Liver Injury (DILI):  0.938
AMES Toxicity:  0.056
Rat Oral Acute Toxicity:  0.42
Maximum Recommended Daily Dose:  0.097
Skin Sensitization:  0.622
Carcinogencity:  0.922
Eye Corrosion:  0.034
Eye Irritation:  0.112
Respiratory Toxicity:  0.935

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

  Natural Product: NPC124277

Natural Product ID:  NPC124277
Common Name*:   REFDVDWXWAWAOK-VNHYZAJKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  REFDVDWXWAWAOK-VNHYZAJKSA-N
Standard InCHI:  InChI=1S/C15H20O3/c1-9-5-4-6-15(3)13(18-15)8-11-10(2)14(16)17-12(11)7-9/h5,12-13H,4,6-8H2,1-3H3/t12-,13+,15-/m1/s1
SMILES:  CC1=CCC[C@]2(C)[C@H](CC3=C(C)C(=O)O[C@@H]3C1)O2
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:0001283] Terpene lactones

*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
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits Spanish DOI[10.1021/jf00010a019]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. DOI[10.1021/jf00016a013]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Germany DOI[10.1021/jf00016a013]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Italy DOI[10.1021/jf00016a013]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits Turkey DOI[10.1111/j.1745-4557.2003.tb00250.x]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. DOI[10.17660/ActaHortic.2003.610.16]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[10794642]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[10820090]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[11754554]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[15315387]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[16076125]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[16920856]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[19358604]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[21190690]
NPO6674 Burkholderia ambifaria Species Burkholderiaceae Bacteria n.a. n.a. n.a. PMID[22988812]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. New Zealand PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Germany PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[2413754]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. PMID[24216090]
NPO11257 Momordica dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[30673219]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[9542132]
NPO11097 Lepidium apetalum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11097 Lepidium apetalum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11257 Momordica dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11097 Lepidium apetalum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11257 Momordica dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11097 Lepidium apetalum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9307 Ficus indica Species Ficidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16164 Podocarpus urbani Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO936 Pinalia spicata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5827 Dalea tuberculata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10738 Cotoneaster horizontalis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5013 Loranthus spicatus Species Loranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11555 Pterocaulon purpurascens Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5392 Pachycereus pecten-aboriginum Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11257 Momordica dioica Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6256 Eucalyptus umbra Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12891 Minasia alpestris Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3740 Trisetum flavescens Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1185 Stereocaulon strictum Species Stereocaulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3385 Cassine transvaalensis Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO468 Dryopteris oligophlebia Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9512 Phlomis fruticosa Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11097 Lepidium apetalum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17386 Securidaca longepedunculata Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6674 Burkholderia ambifaria Species Burkholderiaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO9928 Cephalaria cilicica Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19898 Stevia lucida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9040 Elsinoe annonae Species Elsinoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12998 Salvia rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11815 Mikania hirsutissima Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12192 Coronilla scorpioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10399 Manfreda virginica Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7345 Ptilonia magellanica Species Bonnemaisoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7048 Eucalyptus rariflora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8484 Codonopsis lanceolata Species Campanulaceae 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 NPC124277 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 NPC124277 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