Structure

Physi-Chem Properties

Molecular Weight:  262.19
Volume:  306.986
LogP:  3.824
LogD:  3.503
LogS:  -3.589
# Rotatable Bonds:  9
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.359
Synthetic Accessibility Score:  3.781
Fsp3:  0.471
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:  -4.447
MDCK Permeability:  3.291328175691888e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.714
30% Bioavailability (F30%):  0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.935
Plasma Protein Binding (PPB):  94.35478973388672%
Volume Distribution (VD):  2.545
Pgp-substrate:  6.304244041442871%

ADMET: Metabolism

CYP1A2-inhibitor:  0.224
CYP1A2-substrate:  0.111
CYP2C19-inhibitor:  0.097
CYP2C19-substrate:  0.822
CYP2C9-inhibitor:  0.049
CYP2C9-substrate:  0.924
CYP2D6-inhibitor:  0.073
CYP2D6-substrate:  0.787
CYP3A4-inhibitor:  0.24
CYP3A4-substrate:  0.298

ADMET: Excretion

Clearance (CL):  6.725
Half-life (T1/2):  0.528

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.778
Drug-inuced Liver Injury (DILI):  0.437
AMES Toxicity:  0.104
Rat Oral Acute Toxicity:  0.076
Maximum Recommended Daily Dose:  0.196
Skin Sensitization:  0.215
Carcinogencity:  0.866
Eye Corrosion:  0.52
Eye Irritation:  0.919
Respiratory Toxicity:  0.841

Download Data

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

  Natural Product: NPC484891

Natural Product ID:  NPC484891
Common Name*:   APGBIBLWIBJPQD-SDNWHVSQSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  APGBIBLWIBJPQD-SDNWHVSQSA-N
Standard InCHI:  InChI=1S/C17H26O2/c1-7-14(4)11-12-17(19-16(6)18)15(5)10-8-9-13(2)3/h7,9,11,17H,1,5,8,10,12H2,2-4,6H3/b14-11+
SMILES:  C=C/C(=C/CC(C(=C)CCC=C(C)C)OC(=O)C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10491749
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
NPO11702 Plexaurella grisea Species Plexauridae Eukaryota n.a. n.a. n.a. PMID[11325216]
NPO11702 Plexaurella grisea Species Plexauridae 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
NPT168 Cell Line P388 Mus musculus IC50 = 2.5 ug.mL-1 PMID[11325216]
NPT81 Cell Line A549 Homo sapiens IC50 = 5.0 ug.mL-1 PMID[11325216]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 5.0 ug.mL-1 PMID[11325216]
NPT170 Cell Line SK-MEL-28 Homo sapiens IC50 = 5.0 ug.mL-1 PMID[11325216]

☑ 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 NPC484891 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 NPC484891 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