Structure

Physi-Chem Properties

Molecular Weight:  268.11
Volume:  296.674
LogP:  4.161
LogD:  2.799
LogS:  -3.494
# Rotatable Bonds:  1
TPSA:  60.69
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.541
Synthetic Accessibility Score:  3.795
Fsp3:  0.176
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:  -4.943
MDCK Permeability:  1.4392789125849959e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.43
30% Bioavailability (F30%):  0.051

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.082
Plasma Protein Binding (PPB):  95.56605529785156%
Volume Distribution (VD):  0.903
Pgp-substrate:  2.0494065284729004%

ADMET: Metabolism

CYP1A2-inhibitor:  0.878
CYP1A2-substrate:  0.721
CYP2C19-inhibitor:  0.736
CYP2C19-substrate:  0.26
CYP2C9-inhibitor:  0.906
CYP2C9-substrate:  0.855
CYP2D6-inhibitor:  0.385
CYP2D6-substrate:  0.464
CYP3A4-inhibitor:  0.599
CYP3A4-substrate:  0.22

ADMET: Excretion

Clearance (CL):  11.333
Half-life (T1/2):  0.625

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.936
AMES Toxicity:  0.769
Rat Oral Acute Toxicity:  0.849
Maximum Recommended Daily Dose:  0.934
Skin Sensitization:  0.958
Carcinogencity:  0.66
Eye Corrosion:  0.884
Eye Irritation:  0.957
Respiratory Toxicity:  0.943

Download Data

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

  Natural Product: NPC156599

Natural Product ID:  NPC156599
Common Name*:   BRMAAADEEFMXPX-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  BRMAAADEEFMXPX-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C17H16O3/c1-11(2)5-7-13-9-16(19)14(8-6-12(3)4)15(10-18)17(13)20/h9,18-20H,1,3,10H2,2,4H3
SMILES:  C=C(C)C#Cc1cc(c(C#CC(=C)C)c(CO)c1O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11000049
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000136] Hydroquinones

*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
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. PMID[12003003]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota leaves n.a. n.a. PMID[15568789]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. Isla Isabel (Gulf of California, Mexico) n.a. PMID[19007287]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh leaves n.a. n.a. PMID[19778089]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota fresh fruits n.a. n.a. PMID[20092288]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. PMID[25565282]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Mycelia n.a. n.a. PMID[26807743]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota Fruiting Bodies n.a. n.a. PMID[33246107]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. PMID[9784163]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18114 Cyclamen repandum Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21490 Hypoxylon fragiforme Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24508 Aspergillus brunneus Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1493 Hericium erinaceus Species Hericiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4994 Pachysandra procumbens Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19031 Thymus marschallianus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21431 Rapanea laetevirens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19990 Axinyssa isabela Species Halichondriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21301 Stereum hirsutum Species Stereaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21558 Ormosia sumatrana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18857 Pteronia eenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20485 Cussonia arborea Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17541 Andryala pinnatifida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20276 Burasaia madagascariensis Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9838 Eucalyptus maideni Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18460 Trema dielsiana Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20747 Stictocardia campanulata Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13404 Plantago subulata Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21238 Berberis tabiensis Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19796 Azolla filiculoides Species Azollaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19907 Helicobasidium mompa Species Helicobasidiaceae 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 NPC156599 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 NPC156599 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