Structure

Physi-Chem Properties

Molecular Weight:  302.22
Volume:  338.478
LogP:  3.35
LogD:  2.674
LogS:  -0.755
# Rotatable Bonds:  2
TPSA:  37.3
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.772
Synthetic Accessibility Score:  4.779
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.669
MDCK Permeability:  1.908105878101196e-05
Pgp-inhibitor:  0.594
Pgp-substrate:  0.099
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.905
30% Bioavailability (F30%):  0.029

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.645
Plasma Protein Binding (PPB):  69.60173797607422%
Volume Distribution (VD):  0.836
Pgp-substrate:  24.958553314208984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.52
CYP2C19-inhibitor:  0.031
CYP2C19-substrate:  0.705
CYP2C9-inhibitor:  0.085
CYP2C9-substrate:  0.045
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.04
CYP3A4-inhibitor:  0.963
CYP3A4-substrate:  0.616

ADMET: Excretion

Clearance (CL):  11.629
Half-life (T1/2):  0.273

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.618
Drug-inuced Liver Injury (DILI):  0.048
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.895
Maximum Recommended Daily Dose:  0.928
Skin Sensitization:  0.294
Carcinogencity:  0.955
Eye Corrosion:  0.101
Eye Irritation:  0.136
Respiratory Toxicity:  0.982

Download Data

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

  Natural Product: NPC258439

Natural Product ID:  NPC258439
Common Name*:   HKFZBGDCJPXQHN-WAPOTWQKSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  HKFZBGDCJPXQHN-WAPOTWQKSA-N
Standard InCHI:  InChI=1S/C20H30O2/c1-5-18(2)9-8-16-14(10-18)6-7-17-19(3,13-21)11-15(22)12-20(16,17)4/h5,10,16-17,21H,1,6-9,11-13H2,2-4H3/t16-,17-,18-,19-,20+/m1/s1
SMILES:  C=C[C@]1(C)CC[C@@H]2C(=C1)CC[C@@H]1[C@](C)(CC(=O)C[C@@]21C)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10494596
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids

*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
NPO5326 Knema furfuracea Species Myristicaceae Eukaryota n.a. n.a. n.a. PMID[8254357]
NPO6066 Graphium sarpedon Species Papilionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5326 Knema furfuracea Species Myristicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4903 Duroia hirsuta Species Rubiaceae 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 NPC258439 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 NPC258439 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